I orginally had the same problem in my car as well. Ended up using RCA Splitter plugs, typical stereo mini-jack to rca's going to a set of splitters plugged into the front amp. Then from the splitter going to a 10inch Kenwood sub at the back.
I really reccomend using line out on a sound card. If you drive an amplified signal into line in on an amp you can put quite a lot of stress on them and damage components.
(The joys of having a certificate in sound engineering)