My remote start has an extra output that only has power when the unit is on. I wired in a normally closed relay to the ignition power wire on the anti-theft box and used that extra output as the trigger. When I use the remote start to start the truck, it energizes the relay and opens the ingition power circuit of the anti-theft module. This way the anti-theft module does not know that the engine is running. When I put my key in the ignition and let the truck power itself the remote start cuts off and the relay closes so everything is back to normal.
If I could change anything I would do this to whatever wire tells the GEM that the truck is running also. Even though the remote works and unlocks the door with the car running, the interior lights don't come on when you unlokc the doors like they normally would.
I can't seem to find my CD so I can't tell you what color wire it is, but I'm sure somebody has a diagram for the anti-theft system.