diff --git a/fle/env/gym_env/config.py b/fle/env/gym_env/config.py
index f3fd0ab3..c4495d64 100644
--- a/fle/env/gym_env/config.py
+++ b/fle/env/gym_env/config.py
@@ -29,6 +29,7 @@ class GymEvalConfig:
     task: Optional[TaskABC] = None
     agent_cards: Optional[List[AgentCard]] = None
     env_id: Optional[str] = None  # Gym environment ID for registry-based creation
+    instance_id: Optional[int] = None  # Which container to use for this evaluation
 
     def __post_init__(self):
         if self.task is None and hasattr(self.agents[0], "task"):
diff --git a/fle/env/gym_env/registry.py b/fle/env/gym_env/registry.py
index 931d7401..28ca5e9e 100644
--- a/fle/env/gym_env/registry.py
+++ b/fle/env/gym_env/registry.py
@@ -60,7 +60,7 @@ class FactorioGymRegistry:
                 goal_description = task_config.get(
                     "goal_description", f"Task: {task_key}"
                 )
-                num_agents = task_config.get("num_agents", 1)
+                num_agents = task_config["num_agents"]
                 # Register the environment
                 self.register_environment(
                     env_id=task_key,
@@ -130,7 +130,7 @@ class FactorioGymRegistry:
 _registry = FactorioGymRegistry()
 
 
-def make_factorio_env(env_spec: GymEnvironmentSpec) -> FactorioGymEnv:
+def make_factorio_env(env_spec: GymEnvironmentSpec, instance_id: int) -> FactorioGymEnv:
     """Factory function to create a Factorio gym environment"""
 
     # Create task from the task definition
@@ -146,7 +146,8 @@ def make_factorio_env(env_spec: GymEnvironmentSpec) -> FactorioGymEnv:
             ips, udp_ports, tcp_ports = get_local_container_ips()
             if len(tcp_ports) == 0:
                 raise RuntimeError("No Factorio containers available")
-            address, tcp_port = ips[0], tcp_ports[0]
+            address = ips[instance_id]
+            tcp_port = tcp_ports[instance_id]
 
         common_kwargs = {
             "address": address,
diff --git a/fle/env/gym_env/run_eval.py b/fle/env/gym_env/run_eval.py
index b73d00d3..3dafc00e 100644
--- a/fle/env/gym_env/run_eval.py
+++ b/fle/env/gym_env/run_eval.py
@@ -1,4 +1,3 @@
-import argparse
 import asyncio
 import json
 import multiprocessing
@@ -17,6 +16,10 @@ from fle.agents.gym_agent import GymAgent
 from fle.commons.cluster_ips import get_local_container_ips
 from fle.commons.db_client import create_db_client
 from fle.eval.algorithms.independent import get_next_version
+from fle.eval.tasks import TaskFactory
+from fle.env.utils.controller_loader.system_prompt_generator import (
+    SystemPromptGenerator,
+)
 
 load_dotenv()
 
@@ -55,8 +58,7 @@ async def run_trajectory(run_idx: int, config: GymEvalConfig):
     """Run a single gym evaluation process"""
     db_client = await create_db_client()
 
-    # Create gym environment using gym.make()
-    gym_env = gym.make(config.env_id)
+    gym_env = gym.make(config.env_id, instance_id=config.instance_id)
 
     log_dir = os.path.join(".fle", "trajectory_logs", f"v{config.version}")
     runner = GymTrajectoryRunner(
@@ -70,42 +72,31 @@ async def run_trajectory(run_idx: int, config: GymEvalConfig):
     await db_client.cleanup()
 
 
-async def main():
-    parser = argparse.ArgumentParser()
-    pkg = importlib.resources.files("fle")
-    default_config = pkg / "eval" / "algorithms" / "independent" / "gym_run_config.json"
-    parser.add_argument(
-        "--run_config",
-        type=str,
-        help="Path of the run config file",
-        default=str(default_config),
-    )
-    args = parser.parse_args()
-
+async def main(run_config, offset):
     # Read and validate run configurations
-    run_configs = get_validated_run_configs(args.run_config)
-
+    run_config = get_validated_run_configs(run_config)
+    pkg = importlib.resources.files("fle")
     # Get starting version number for new runs
     base_version = await get_next_version()
     version_offset = 0
 
     # Create and start processes
     processes = []
-    for run_idx, run_config in enumerate(run_configs):
+    for run_idx, run_config in enumerate(run_config):
         # Get environment info from registry
         env_info = get_environment_info(run_config.env_id)
         if env_info is None:
             raise ValueError(f"Could not get environment info for {run_config.env_id}")
-
-        # Create gym environment to get task and instance
-        gym_env = gym.make(run_config.env_id)
-        task = gym_env.unwrapped.task
-        instance = gym_env.unwrapped.instance
+        task = TaskFactory.create_task(env_info["task_config_path"])
+        generator = SystemPromptGenerator(str(pkg / "env"))
         # Create agents and their agent cards
         agents = []
         agent_cards = []
-        for agent_idx in range(instance.num_agents):
-            system_prompt = instance.get_system_prompt(agent_idx)
+        num_agents = env_info["num_agents"]
+        for agent_idx in range(num_agents):
+            system_prompt = generator.generate_for_agent(
+                agent_idx=agent_idx, num_agents=num_agents
+            )
             agent = GymAgent(
                 model=run_config.model,
                 system_prompt=system_prompt,
@@ -132,13 +123,13 @@ async def main():
         config = GymEvalConfig(
             agents=agents,
             version=version,
-            version_description=f"model:{run_config.model}\ntype:{task.task_key}\nnum_agents:{instance.num_agents}",
+            version_description=f"model:{run_config.model}\ntype:{task.task_key}\nnum_agents:{num_agents}",
             exit_on_task_success=run_config.exit_on_task_success,
             task=task,
             agent_cards=agent_cards,
             env_id=run_config.env_id,
+            instance_id=run_idx + offset,
         )
-
         # Ensure agent cards are properly set for a2a functionality
         assert config.agent_cards is not None
 
diff --git a/fle/env/instance.py b/fle/env/instance.py
index 35b203a5..a4759c06 100644
--- a/fle/env/instance.py
+++ b/fle/env/instance.py
@@ -271,18 +271,9 @@ class FactorioInstance:
         """
         execution_path = Path(os.path.dirname(os.path.realpath(__file__)))
         generator = SystemPromptGenerator(str(execution_path))
-        multiagent_str = ""
-        if self.num_agents > 1:
-            player_idx = agent_idx + 1
-            multiagent_str = (
-                f"## MULTIAGENT INSTRUCTIONS\n"
-                f"You are Agent {player_idx} out of {self.num_agents} agent(s) in the game. "
-                f"Follow your specific instructions given to you by the task."
-                f"Use the send_message() tool regularly to communicate with other agents about your current activities and any challenges you encounter. "
-                f"Start each program with a send_message() call to explain what you are doing. "
-                f"End each program with a send_message() call to confirm your actions. If your program errors out prior to send_message() being called, the message will not be sent. "
-            )
-        return generator.generate(multiagent_str)
+        return generator.generate_for_agent(
+            agent_idx=agent_idx, num_agents=self.num_agents
+        )
 
     def connect_to_server(self, address, tcp_port):
         try:
diff --git a/fle/env/protocols/mcp/resources.py b/fle/env/protocols/mcp/resources.py
index dc42b280..3977c717 100644
--- a/fle/env/protocols/mcp/resources.py
+++ b/fle/env/protocols/mcp/resources.py
@@ -1,7 +1,6 @@
 import json
-import os
-from pathlib import Path
 from typing import Dict
+import importlib.resources
 
 from fle.env.utils.controller_loader.system_prompt_generator import (
     SystemPromptGenerator,
@@ -220,11 +219,7 @@ async def get_recipe(name: str) -> Dict:
 async def get_all_api_docs(method: str):
     """Get all API docs"""
 
-    execution_path = (
-        Path(os.path.dirname(os.path.realpath(__file__))).parent
-        / Path("env")
-        / Path("src")
-    )
+    execution_path = importlib.resources.files("fle") / "env"
     generator = SystemPromptGenerator(str(execution_path))
     return generator.manual(method)
 
@@ -234,13 +229,9 @@ async def get_all_api_docs(method: str):
 async def get_all_api_schema():
     """Get all API docs"""
 
-    execution_path = (
-        Path(os.path.dirname(os.path.realpath(__file__))).parent
-        / Path("env")
-        / Path("src")
-    )
+    execution_path = importlib.resources.files("fle") / "env"
     generator = SystemPromptGenerator(str(execution_path))
     schema = (
         generator.schema() + "\n\n" + generator.types() + "\n\n" + generator.entities()
     )
-    return schema.replace("env.src.", "")
+    return schema
diff --git a/fle/env/protocols/mcp/tools.py b/fle/env/protocols/mcp/tools.py
index 9e82a880..46bfb29a 100644
--- a/fle/env/protocols/mcp/tools.py
+++ b/fle/env/protocols/mcp/tools.py
@@ -1,6 +1,5 @@
-import os
-from pathlib import Path
 from typing import Dict
+import importlib.resources
 
 from mcp.server.fastmcp import Image
 from fle.env.entities import Position
@@ -187,11 +186,7 @@ async def schema() -> str:
     """
     Get the full API object model for writing code so that you can interact with Factorio.
     """
-    execution_path = (
-        Path(os.path.dirname(os.path.realpath(__file__))).parent
-        / Path("env")
-        / Path("src")
-    )
+    execution_path = importlib.resources.files("fle") / "env"
     # Generate the documentation
     generator = SystemPromptGenerator(str(execution_path))
     return f"\n\n{generator.types()}\n\n{generator.entities()}"
@@ -206,11 +201,7 @@ async def manual(name: str) -> str:
         name: Name of the method to get documentation for (must be a valid API method)
     """
     # Get the list of available agent tools by checking directories in the agent directory
-    execution_path = (
-        Path(os.path.dirname(os.path.realpath(__file__))).parent
-        / Path("env")
-        / Path("src")
-    )
+    execution_path = importlib.resources.files("fle") / "env"
     agent_tools_path = execution_path / "tools" / "agent"
 
     # Verify the agent_tools_path exists
diff --git a/fle/env/protocols/mcp/unix_tools.py b/fle/env/protocols/mcp/unix_tools.py
index a72adf7a..ad593651 100644
--- a/fle/env/protocols/mcp/unix_tools.py
+++ b/fle/env/protocols/mcp/unix_tools.py
@@ -3,9 +3,9 @@ Unix-like tools for code introspection in Factorio Learning Environment
 """
 
 import glob
-import os
 import re
 from pathlib import Path
+import importlib.resources
 
 from fle.env.utils.controller_loader.system_prompt_generator import (
     SystemPromptGenerator,
@@ -15,12 +15,7 @@ from fle.env.protocols.mcp import mcp
 
 def _get_tools_base_path() -> Path:
     """Get the base path to the tools directory"""
-    return (
-        Path(os.path.dirname(os.path.realpath(__file__))).parent
-        / Path("env")
-        / Path("src")
-        / "tools"
-    )
+    return importlib.resources.files("fle") / "env" / "tools"
 
 
 @mcp.tool()
@@ -505,11 +500,7 @@ async def man(command: str) -> str:
 
         # If no dedicated doc file, try to generate from the implementation
         try:
-            execution_path = (
-                Path(os.path.dirname(os.path.realpath(__file__))).parent
-                / Path("env")
-                / Path("src")
-            )
+            execution_path = importlib.resources.files("fle") / "env"
             generator = SystemPromptGenerator(str(execution_path))
             manual = generator.manual(command)
             if manual:
diff --git a/fle/env/utils/controller_loader/system_prompt_generator.py b/fle/env/utils/controller_loader/system_prompt_generator.py
index a030ed76..1334f720 100644
--- a/fle/env/utils/controller_loader/system_prompt_generator.py
+++ b/fle/env/utils/controller_loader/system_prompt_generator.py
@@ -43,6 +43,20 @@ class SystemPromptGenerator:
             f"Here is the manual for the tools available to you\n\n{manual_defs}"
         )
 
+    def generate_for_agent(self, agent_idx: int = 0, num_agents: int = 1) -> str:
+        multiagent_str = ""
+        if num_agents > 1:
+            player_idx = agent_idx + 1
+            multiagent_str = (
+                f"## MULTIAGENT INSTRUCTIONS\n"
+                f"You are Agent {player_idx} out of {num_agents} agent(s) in the game. "
+                f"Follow your specific instructions given to you by the task."
+                f"Use the send_message() tool regularly to communicate with other agents about your current activities and any challenges you encounter. "
+                f"Start each program with a send_message() call to explain what you are doing. "
+                f"End each program with a send_message() call to confirm your actions. If your program errors out prior to send_message() being called, the message will not be sent. "
+            )
+        return self.generate(multiagent_str)
+
     def manual(self, *args):
         try:
             return ManualGenerator.generate_manual(
diff --git a/fle/run.py b/fle/run.py
index 9d06e598..16596ec0 100644
--- a/fle/run.py
+++ b/fle/run.py
@@ -43,12 +43,8 @@ def fle_cluster(args):
 
 def fle_eval(args):
     try:
-        config_path = Path(args.config)
-        sys.argv = ["run_eval", "--run_config", str(config_path)]
-    except TypeError:
-        sys.argv = ["run_eval"]
-    try:
-        asyncio.run(run_eval())
+        config_path = str(Path(args.config))
+        asyncio.run(run_eval(config_path, args.offset))
     except Exception as e:
         print(f"Error: {e}", file=sys.stderr)
         sys.exit(1)
@@ -87,6 +83,11 @@ Examples:
     )
     parser_eval = subparsers.add_parser("eval", help="Run experiment")
     parser_eval.add_argument("--config", required=False, help="Path to run config JSON")
+    parser_eval.add_argument(
+        "--offset",
+        type=int,
+        help="Offset to add to instance_id selection",
+    )
     args = parser.parse_args()
     if args.command:
         fle_init()