Depends on the AV amp. My last AV amp (a yamaha) was a bit picky about how it played a stereo source, it was either 5.1 or straight bypass to FL/FR.
My current AV amp Arcam will only play a stereo source to one of 3 options 1, FL/FR 2, FL/FR+sub (which is how I usually use it) 3, Bypass to...