In PluralEyes 2, you were able to add markers is certain clips had trouble synching.
Use this option when you know two clips should sync and you can identify an approximate sync point. A sync point can be one of usual events that are used for a manual sync: a camera flash or other distinct visual event; a short loud audio event; a hand clap; a slate. The difference between doing the sync manually and using markers is that you only need to identify the sync points approximately (to within about 30-60 seconds) and PluralEyes will refine the sync to the exact frame.
To use markers, go to the sync point in each clip and add a marker. Give matching markers in the two clips identical names. Select the Use markers option and run PluralEyes in the usual way. It will read the markers to determine the approximate sync and then refine it from there.
You can have more than one marker for PluralEyes as long as you name them appropriately. For example, suppose you have three clips (A, B and C) from a music video. B covers the whole song but A is just the beginning and C just the end. You could put two markers on clip B named "start" and "end" and corresponding markers "start" in A and "end" in C. PluralEyes will use the "start" markers to sync A-B and the "end" markers to sync B-C.
Is this still the case with version 3? and if so how do I go about it with FCPX?