"there any way to hook up my audio out on my EPIA board to the speaker wires so that the stock amp can power the speakers?? (my head unit will be removed"
Probably. I believe crutchfield.com sells an adapter that allows you to use the stock amp with an aftermarket head unit. Adapt it for your carputer use.
"The area that I am concerned about is the fact that a stereo output from the computer has 2 wires (one for left and one for right)"
Been awhile since I spliced a mini 1/8" cable, but I'm pretty sure there were at 3 if not 4 wires. R+, L+, and either a common ground or L/R -. Either way, the 1/8" to rca adapter should take care of it.