Nelson, thanks for the link. After reading Slickmans post, it seems he had the same problem that I have. Regarding the wiring configuration, here's what I know; and it ain't all that much so don't get too excited.
The C5's have 3 plugs (actually 4, but two are connected together) that connect to the HU. One plug (c1 and c2) is the standard GM radio harness plug. It connects power, remote amp, power antenna, and the front/rear left/right speaker outputs. I have this plug wired to the HU just like you would normally wire in any aftermarket HU.
The two remaining plugs (c3 and c4) are specific to the C5 bose unit. The c3 plug is supposed to receive signal from the HU and send it to the Bose Signal Processor, which processes the signal and sends it back on the same plug. The signal is then supposed to go out via the C4 plug to the subs in the doors. The only thing I have connected here is the yellow (common, not ground) wire from the c3 plug to speaker common on c1/2. If this isn't done the subs won't fire at all, regardless of time
When my subs go out the rest of the speakers still work. This leads me to believe there's a common link between the pair of subs. All I can think of is the Bose Signal processor and power/ground. If the amps on the subs are connected to a common ground, losing that ground would make them both go out. Or, if the Signal processor uses a relay that doens't fire it could make the system go out. What I don't know is if the subs will fire if the Signal process is turned off.
I know it's a long rant, but I've been dealing with this issue for the last month + and have been getting nowhere. I'm almost ready to shove the system out the door and rewire everything.