I bought an aftermarket radio harness for the Grand Cherokee and spliced my existing speaker wires into that. I then used a low-power amp with RCA inputs as the "input" for the stock amp. diagram:
CARPUTER --> 100W AMP W/ RCA INPUT --> AFTERMARKET WIRING HARNESS --> STOCK JEEP HEADUNIT CONNECTOR --> STOCK JEEP AMP --> 10-SPEAKER INFINITY SYSTEM
People say they worry about distortion with 2 amps, but the stock setup already includes 2 amplification sources as it is. For more info check out:
http://www.wjjeeps.com/audioupgrade.htm