I have an 03 sedan, every speaker works besides the subwoofer. I have tried:
A different amp
A different subwoofer
A different radio

So I'm assuming the problem is in the wiring or a fuse. I looked at the service manual and it says theres a seperate fuse going to the subwoofer, but I've checked all 3 fuse boxes and see nothing about it. Any ideas?

 

Well, the 03 sedan's subwoofer has its own amp, not shared with the other speakers at all. It shares its input signal with the speakers, so your problem is probably with the bose subwoofer amp.

 

You're absolutely right. I got it fixed early this morning The relay inside that mini amp(under the subwoofer) was loose. I stuffed some paper in the amp casing and put it back up there. Works perfectly now.

During all my research, I couldn't find anything about a 2nd amp or anything even remotely related.