Selecting audio channels during capturing

I am in the process of capturing a interview style documentary that was shot with a Panasonic AG-DVX100B. The interviews that were shot on location used a handheld wireless microphone connected to line 1. Normally, I would set the capture setup to only capture line 1 of the audio so that the built-in camera mic on line 2 would not be captured and create an echo. I would then capture the entire day's shoot into one clip. The shoot is about 45 minutes in total.
During this particular day's shoot we shot some footage in the car using only the built-in camera mic. The camera was still set to use the wireless receiver on line 1, so only line 2 has audio (from the camera mic). So as you can figure, when I captured my normal way with only line 1, there was no audio for the car scenes.
The audio from the car scene was recorded fine on line 2 so now I need to come up with a different process for capturing this show... and maybe reconsider the way way I capture all together. I have not started editing so it's okay to recapture at this point.
My question is:
1. Should I capture each of the three locations seperatly with different audio settings and do a batch capture? ie; Location 1 (line 1 for handheld mic) Car (line 2 for camera mic) and Location 2 (line 1 for handheld mic).
2. Do I capture both line 1 and 2 into one 45 minute clip and select the audio channel that I want from within FCP?
3. If answer 2 is the recommendation, how do I do that without having to deselect an audio channel in each edit in the timeline.
Thanks in advance for the assistance!

go for option 2,
you can de-select the errant audio track from the source side when you create your sequence so you don't have to do it to all edits. thats one of the joys of editing!
you may find you have some good sound on the other mike though don't just throw it away
best regards
andy

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