Best Way to Sync Audio?

I'm using Final Cut Pro (v6.0.3) to edit a short film that was shot with the RED Camera. The Log and Transfer ingest method seems to be working great, so I'm happy with that. My question is about the workflow for audio.

The audio during the shoot was captured on a separate digital recording device. They used a clapboard slate, so I'll be able to sync the audio with the video, but how do I keep it in sync? Right now, I have Pro Res QuickTime files for the video and .wav files for the audio. I can sync them in the timeline, but the source files themselves will still be separate. I want to avoid syncing, exporting every synced take as a QT, and then reimporting them. Does anyone have a suggestion for how to sync the footage and keep it in sync? This may be more of a Final Cut Pro question than a RED question, but I'd appreciate any advice you could offer.

Thanks,
Conor