If you can, you want the interview to be a conversation, so it will inevitably meander.
Transcripts can help. You can either do it yourself or hire it done. There are quite a few COW members who do it. Also, Production Transcripts is good at about $2.50/minute with timecode. One way to DIY is to listen to each line, repeat it into software like Naturally Speaking, and hope for the best. It’s still tedious.
Best, of course, is to start the process of noting the timecode of the good soundbites during the interview. There are expensive solutions for this, but you can also just use time-of-day timecode and note the time. If you have an assistant he/she can help with this.
I was hoping that MovieSlate would help me with this, but I haven’t been able to find a way to use it effectively. I wanted the interviewer to be able to tap to record the timecode at every good soundbite, but it turns out you have to tap, enter something, then tap again. An assistant who is getting a verbal or physical cue from the interviewer might be able to handle that, but it’s too distracting for an interviewer who is trying to maintain human contact.