Hmm, if you have the 6 mono wavs (ripped from an ac3, I would imagine) you could use something like Audacity (freeware) to recombine them into a 6-channel uncompressed wav to use in your project. This would spare some audio quality as you wouldn't be recompressing to ac3 until the final output. Audacity will let you silence individual tracks (essentially giving you 4.1 output if you silence the center track). For my recent edit I just used Audacity to export the original ac3 to 6 wavs. I like the ease of having each track with individualy key-framable volume levels. I then output the final audio as a new uncompressed 6-channel wav from premiere, and used audacity again with ffmpeg to convert it to ac3.
I don't use Vegas or any derivative, so I'm not sure of the audio formats it is capable of using. So I guess it would depend on whether that particular program can work with 6-channel uncompressed wavs.