I'm currently working on a transcription program (well, i'm working on an update...)
BWF is the easiest format, as it contains TC so things cannot go wrong.
The windows version of my application already supports BWF, the mac will in a week or so.
If you like, i can make a QT to BWF converter as well, so if you export QT's from FCP and run them trough my app, you end up with BWF's that are fool proof.
The way it is now you either have to enter the TC on one of the frames (most of the time the start frame), or have a stereo file where one of the channels contains LTC.
Also works, but normally you don't have LTC in your ingested material.
if you digitize and have a channel to spare, that's also an option.
have a look at my site for some demos...