newbie needs some help with remote start

I guess I should start off by saying I've never done anything like this at all to my vehicle and now I'm wondering why I got this idea to being with.

I have a CrimeStopper RS-800III that I'm trying to install.  I have it hooked up along with the Passlock I bypass module.  When the car tries to start the Theft light blinks and it will not start.  Obviously this is because the Passlock I isn't hooked up correctly. 

What's scaring me is when I start the car with the KEY the "check engine" light comes on and the car runs poorly.......  I've checked the 2 Ignition wires and they're tapped into, not cut.  I also found 2 smaller black wires in the same harness, are these grounds for the Ignition or are they for the 2 constant 12v wires?  I tapped into them, as I thought they were the bulb test wires, turns out that wire is futher up. 

Any ideas?  Even with the remote start unit unplugged and starting it with the key the Check Engine light still comes on.  :(

Thanks for any help, I appreciate it.

Very close, 1997 Pontiac Grand AM SE.  Basically the same as a Sunfire.

I'm not 100% positive which wire is the bulb test wire b/c there are 3 small black wires in the ignition harness.  If I can get the check engine light off then I can go back and work on the Passlock system.

I have the negative battery cable removed right now and I'll post the result.

Thanks for your help, I appreciate it. :)

OK I left the cable disconnected for 15 mintues.  Started the engine and it was off for at least a few mintues.  The engine ran very rough and there was a decent amount of smoke coming out the back.   I've never seen my car smoke before!  Could this be because of all the short cranks it's been making without actually starting?  Would that cause a check engine light?

Thanks for any help.