I'm beginning a documentary, shooting on the 5d, with external sound to an h4N. I'm expecting a lot of footage, so I don't want to convert to ProRes422 right away; as of now I am archiving my CF cards (video) and SD cards (audio) in folders created each day. I'm also syncing sound with Pluraleyes, in a FCP project file I create daily, again without converting to ProRes.
Since this is a longer-term shoot, my thinking is that I'll wait until FCP X comes out, which will hopefully allow me to edit the 5d's h264 files natively. In the meantime, I am doing the heavy-lifting (at the end of the day syncing sound and doing some basic logging).
The way I've "married" external sound to the 5d video in the past has been this way: I sync the audio and video on a timeline, adjust the levels on each channel, then export one big ProRes422 Quicktime file. I reimport this file and edit from it.
Before I start doing this, and it's worked for me in the past on my admittedly much smaller projects, I was hoping there's someone out there with more experience that might share their workflow with me.
Last summer I filmed a feature film using a 7D on most days on some a 5D and a 7D and the H4n using all 4 channels.
We would make a disk image of each SD card using Disk Utility and each H4n audio card.
Naming each file: MMDD_video##_camA and MMDD_audio##
It did take a long time and yes it was a pain but it was worth it. Each night we made sure that there was a disk image on Directors hard-drive on the DP's (me) hard-drive and the external hard-drive with the producer, that way we can sleep well at night get up 4 hours later and do it all over again, great summer :)
To get the footage in to Final Cut we just mounted the disk image and opened the Log and Transfer, worked like a charm. The Director did the editing, and I did the special effects at a diferent location
When a clip needed special effects work the director can just send over the Final Cut Time line I can then mount the disk image from that day and get to work.
There was no real advantage of doing the same thing with the audio other then we got into the work flow and just did the same thing for all the files from the day.
Hope this helps keep me up to date on how you decide to work,