If the final output is to DVD and BluRay, you’ll probably be creating AC3 files with the 5.1 audio mix. The audio should be bounced to discrete channels. From those audio files, you can create the AC3’s using Compressor or whatever encoder you use.
I think you should import that audio to your FCP project as well, so there is a final completed project to archive for later revisions. Just import the discrete channel mixes to your FCP project. They will be identified with tags in the filename (“Filename.L.aif” for example) so you can place the correct audio on the correct channel. Channel assignment depends on the delivery format so isn’t too critical for you, since the delivery is AC3. If you don’t know what assignments to use, SMPTE302M is what most people expect these days. That is 1.L, 2.R, 3.C, 4.LFE, 5.Ls, 6.Rs, 7.Lt/Lo, 8. Rt/Ro.
So you just need a multi-mono bounce of the audio and you place the channels as needed in FCP and for the AC3 conversion.
IHTH,
JC Boulay
Technical Director
Audio Z
Montreal, Canada
http://www.audioz.com