I replaced my tubes the other day and I'm not certain that I put them all in the right spots. I have a B-52 AT212 and there were two special tubes. One was supposed to go in V5, it said closest to the power tubes, so I put it there. But why is it called V5? Does the rectifier tube not count? And there was supposed to be another special tube in V11 so I assume that was the last tube slot?

The tubes are...
recto, power, power, power, power, balanced phase inverter? (preamp), preamp, preamp, preamp, preamp, preamp, and another preamp that I think is the "ECC81 for V11".

I'm pretty sure I put them in all right, but for some reason my two overdrive channels sound funny now. The clean sounds amazing now though.
V1 is farthest to the RIGHT when looking at the chassis from the back of the amp. You go from right to left with the V number. I suspect that's what tripped you up.

The special tube was the rectifier tube (V11).
Okay, so then I did it correctly. The retube kit I bought was for the AT 100 which is a mirror image of the combo, which is why the tube numbers didn't match.