Using PluralEyes after editing sequence?

Hi guys, I've been editing a short corporate film for a client and I'm using PluralEyes for the first time. I've edited the sequence with the original audio ut now I want to replace that audio with the better recording, so I've added the better audio to my timeline (at the end of the whole sequence), I then attempted to sync it using PluralEyes but it just isn't going as smoothly as I hoped, in fact my results are quite random.

Basically, I've chopped up the audio quite a lot in the edit and I wonder if that has affected it, I probably should have synched all of the audio before I started chopping it all up.

What do you suggest I do now? (See image of my timeline attached).

Thanks!

Alex