Should I connect the aftermarket amp before the wires go into the factory amp or when they come out. Does it matter, does it depend on the amp?

 

I took out the stock amp completly. I'm also still running the stock head unit.

So in answer to your question, connect before you hit the stock amp. If you still need your stock amp to run the cabin speakers, then obviously you would want to keep it in.

I'm not an audio pro, but I do know at least that much.

 

What kind of set up are you running? What type of amp, sub speakers?