6 channels means its 5.1 dolby digital.
you dont need to worry about the 48000hz.TMPGEnc will detect it.
older hardware like a sound card cant handle 48khz,so it would have to be downsampled to 44.1khz.
you just need to convert the ac3 to something that TMPGEnc sees.
the easiest way is to use avi2wav http://www.divx-digest.com/software/avi2wav.html
to extract the wav and use it as the audio source.
regular VirtualDub doesn't produce a true wav,you would have to take the wav and rename the extention to ac3 then convert to wav with another app.
the newest VirtualDubmod might,but i'm not sure.