If there's no amp under the seat, then you probably don't have the "upgrade" stereo system such as came in my '95 XLE.
My XLE had the "upgrade" AM/FM/Cassette system with the the external amp under the seat, but it did NOT have the CD player which was an additional option.
My '95 LE on the other hand had the basic AM/FM/Cassette system with NO amp under the seat and NO CD player either. The head unit had it's own internal amp.
If your stereo worked ok before you plugged the CD player in, then the head unit must have it's own internal amp.
There's like a 13 pin plug on the back of the head unit. Is that where the CD player plugs in?
I still have the head unit from my XLE. I may still have the head unit from my LE in the basement somewhere. I'll look and see and compare the two.
Also, I'm just on my way to my dealer to pick up my Sequoia from being serviced, so while I'm there I'll ask my parts guy if he can give me any info on the stereo hookups.
UPDATE
OK, well, the parts guy at the dealership couldn't tell me ANYTHING.
You may want to post this over in the Audio/Video/Security forum too. I'll see what else I can find out.