All I know of is the 2 amps, one in the tray, and one mounted to the subwoofer.
I had the premium sound without a sub, in a lincoln towncar (1991), and had it with a sub in the SC (90).
The SC amp (in the tray) was black with jbl stickers and had the wire comming out to feed the sub.
The one int he lincoln was silver and had no wire sticking out, and had no jbl stickers, no label other than a ford label...
When I sold the town car, I agreed to put an old pioneer in the lincoln and remove the stock premium sound unit.
I also had to remove the factory amp and use a cable to bypass the factory amp. This cable was available at best buy in the factory cable kit. My guess is that you can use this kit ($15.00) and use the pypass cable (nothing more than 2 amp conectors and a few wires) along with a wiring diagram and make you own "tray amp" to "sub amp" cable using the connectors in that kit.
Keep in mind, I beleive there are actually 3 connections to that sub amp. One on each side f the amp, and another for the power (if I recall correctly)
If someone already has the black amp with jbl stickers outta their car, maybe they can open it up and snap a photo of the amp and you can compare the inards to your amp's inards I bet it's the same amp, only without that wire soldered or connected inside. If so, you can just solder the wire in and be set.
The other solution would be to get the factory black amp with sub output on ebay... Not sure what it would cost though...
Wiring diagrams are available and I might have some somewheres if you need em... and let me know if you want a picture of the inards of the factory stock amp. I can take mine out and apart and snap a pic of the inards if you need em...but it may take a few days, as I'm in the middle of changing motor mounts, and ball joints; which has priority right now ...