I'm just learning FCPX for the first time this week and one of the more confusing functionalities, for my specific case, is the audio syncing for our Zoom Audio.
We shoot with Canon 5D Mark ll's and record our audio using a Zoom recorder. The thing we do, which I guess isn't the best practice, is, instead of stopping the recording audio after each take, we pause the recorder. This gives us one very long continuous track of the entire shooting day. We would normally set that up on a Final Cut Pro 7 sequence with all the footage and use Plural Eyes. Plural Eyes would just line the takes up along the continuous sound and we would cut up the sound with the takes as we needed them. I'm sure it's not the best workflow but it's what we did. In any case, since I cannot see a visual representation of how FCPX has lined up the audio and video, I can't trouble shoot.
I do, however, know that the audio has not synced up on most of the shots. It's most likely because the video takes might overlap some audio takes, which, represented in a sequence timeline, would allow you to see that you have to separate different camera angles onto separate tracks, so they don't obstruct the alignment by bumping into each other. I'm just not sure how that works with FCPX. I would use Plural Eyes to try to troubleshoot this but I'm not sure it would help, since there is not longer that idea of separate video tracks in FCPX that I can see. I guess I'm mostly talking about a multi cam set up.
Sorry if this is not cogent enough. I'm still trying to figure out FCPX but I have a project due soon and I already started it in FCPX. No turning back now and time is ticking!