I’m not sure you can do the re-routing while capture, unless there’s some option in the VTR itself.
Else, the other option is to capture as is. Then place the captured clip in an FCP timeline. Set the sequence settings for 8 tracks all dual mono. Then rearrange the tracks the way you need to. Assign each track’s output where you need it to go. And export the sequence self-contained. Now the tracks will occupy the places you need them to.
Alternately, in QT player 7 there may be a way to arrange the tracks in Movie properties. Maybe.
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Neil Sadwelkar
neilsadwelkar.blogspot.com
twitter: fcpguru
FCP Editor, Edit systems consultant
Mumbai India