The factory system sends speaker level signals to the rear mounted subwoofer amp, with the front mounted external amp enabled or disabled it doesn't matter. The sub signal is off the rear speakers, there is no line level signal sent back there.
Power for the subwoofer amp is the grey wire, that's +12 switched (accessory) and red/black is the 'remote turn on' signal, not constant 12V, so you won't see constant 12V there. There is no constant 12V present on connector W6. It's possible your Sony remote turn on output isn't wired up into the AMP+ signal like it should be. Does the 94 have a power antenna? Does it go up/down automatically?
The signals on W6 are:
- Red (+ RIGHT REAR SPK FROM stereo or front amp)
- Black (+ LEFT REAR SPK FROM stereo or front amp)
- Red/Black (Amp Remote from stereo or front amp)
- Light Green/Black Sub Speaker +
- White (- RIGHT REAR SPK FROM stereo or front amp)
- Yellow (- LEFT REAR SPK FROM stereo or front amp)7.
- N/C
- N/C
- Gray (ACC PWR +12V)
- Light Green/Red SUB -
W6 is a 10 pin connector located in the right rear quarter panel that plugs into the factory sub woofer amp.
That's assuming it is the same wiring as the 96, not sure if anything changed from 94.
If your new amp and sub that you are trying to mount in the rear requires more than about 5 Amps (50 watts RMS w/losses) or requires RCA line level signals, you just can't use the factory wiring.