the thing people have trouble with is the ACC or ignition line with the m1-atx. here is a pic of how to do it:
This is on J-body car I found the pic like 4 minutes after reading your post. You pick a fuse that controls something that can only be turned on if your car is on. I used the windshield wipers. That is tapped into the fuse... the way that i did mine was to wrap the wire around one post of the fuse, then jam it into the fusepanel real tight.
The other two line go straight to the battery, there should be a rubbery thing that you can put a hole through to send wire from the cabin to the engine. Also some people use the car chasis as a ground point. In a few days I will be posting picutres of a few more steps of my carputer and you will see what I am talking about