Here is the radio wiring diagram for a 96 Ford Explorer with the Premium JBL Audio system. There were 4 systems available that year:
Base (4 speakers)
Premium (4 speakers with external amp)
Premium w/CD (4 speakers with external amp, cd changer, rear seat control panel)
JBL (4 speakers and subwoofer, 2 external amps, cd changer, rear seat control panel)
I believe you have the JBL system, as you mentioned a subwoofer.
96FordExplorerJBLAudio.PDF
This diagram is a little complex, but it is labeled well. There are 2 control modules and two control lines (Protocol A and B). I am not familiar with the system. These protocol lines are probably proprietary digital signals, not simply 12v or ground. For this reason, if you want to use the factory amps, I would suggest tapping into the tape or CD changer's audio signals and "hi-jacking" those inputs for your computer's audio. You could hook up a switch to go from CD changer, to computer, for example.
Because the control module provides your input and volume control, the factory amplifier is probably useless without it, unless you can figure out Ford's "Protocols".