I'm not a wizard when it comes to editing or, in this case PluralEyes. At least, not yet. However, I was recently in need of syncing 2 cameras w/audio and a separate audio-only recording and ideally, I wanted 1 beautiful multiclip in my possession when it was all said and done. But how?
What is PluralEyes?
First of all, if you haven't heard of Singular Software's PluralEyes, you need to get on that, man. For real. In a nutshell, PluralEyes (PE) takes multiple sources of cameras and audio and syncs them together like magic. Each camera source should have audio, even if it's shitty, on-board audio so that PE can work it's magic as I believe it does so by comparing the audio from each source.
Getting a multiclip that uses an audio-only source
Ok, so I've got PE running and I'm trying to sync my clips and getting a message saying it can't make a multiclip because one source is audio only. So what do you do? It's pretty simple actually, place each video source and it's respective clips on their own track in a sequence. Do the same with your audio-only clip/s. Note, I think it's best to have your audio-only at the beginning of your sequence. It will look something like the following:

Now, hide each video track and mute everything except for your audio-only. Go to your browser, find your sequence, and Export it using Quicktime. Use the exportsettings in the image and save.

Once you've got a new .mov file of your audio you can ditch your audio-only and place the new .mov on your timeline. Now you're ready for multiclip goodness.
Crap, PluralEyes cannot sync all my clips
After I had everything arranged on my timeline I found that PE kept failing at syncing a couple of clips, even if I created markers and checked the "Use Markers" option. This was standing in the way of my desire for one multiclip and I tried and tried to make it work. I Googled and scoured through Singular's message board and couldn't find anything that helped, but I did notice time and time again on their board that they would ask people to send them their project file and PE's log files. I figured I had tried everything I could think of, why not send an email to support. So that's what I did and boy am I glad!
Singular's support is absolutely first-class! I had a reply within hours of sending my email, from a person, in this case Bruce, telling me they had received my files and would be looking them over shortly. Not much later they had come back asking for more files. After a few exchanges I got my answer which I'll post verbatim here in lieu of paraphrasing and missing something.
Hi Tim,
It looks like the audio recorder was paused for at least 10 seconds or so, and the cameras were started up before the audio was unpaused. The result is that the synced clips will overlap, which is not allowed by FCP, so PluralEyes has to treat those clips as unsynced.
You can see the overlap in the attached overlap1.png. We moved the clips to different tracks, which avoids the overlap problem. That also suggests one workaround: stagger the video clips onto different tracks before syncing.
The second image overlap2.png shows what happens if you split the audio at a point near where it was paused. Everything syncs without overlap, but you can see a gap in the audio where the recording was paused. That suggests another workaround, which is to split the audio track, if you know where the pause points are.
Finally, as a third workaround, you could trim the ends of the video clips a bit before syncing and then restore the trims after the sync.
Regards,
Bruce
When in doubt, stagger, split, or trim
I tried the first method Bruce suggested, staggering my clips a little more to separate tracks and violá! That did the trick. I now had one clean multiclip. I didn't try to the other two methods because I didn't have to, but I included them here hoping that this would help someone down the road. You may not be having the exact same problem I am in terms of overlap, but I'm willing to bet that staggering, splitting up tracks, or trimming them might have an impact in a host of other scenarios you may find yourself in.
Hope this helps!
P.S. Please don't use the comments to ask for help because I'm probably not going to be able to help. Instead try Singular's message board and if you still can't figure it out email their support team.