since you ran the computer's audio directly into the amplifier, you really have no need for the head unit anymore. if the only thing you'll be using it for is the CD player then you would be better off with a USB slot-load DVD/CD drive up front (you can mold it into your dash for a cleaner look).
that being said; if you still insist on keeping the head unit then you have 3 options...
1.) run the computer's audio output into the head unit's aux-in, then run the head unit's RCA output into your amp (or just power your speakers from the head unit itself). this is the best option if you want to keep a head unit.
2.) run the head unit's line-level outputs into the computer/sound card's line-in input. I wouldn't recommend this option unless you want the ability to control your head unit volume from the computer.
3.) use an RCA input selector to switch amplifier input sources (head unit / computer). this option might get tiring after a while
