Hi Leon
I don’t know if my workflow is any better then yours, but we use Plural Eyes for just about every project we do – from wedding films to conferences as we record our main sound usually from digital audio recorders, and use camera audio as a guide.
I start my projects in Premiere, and generally stay in Premiere, essentially using Plural Eyes more as a plugin on the Premiere timeline.
Here are my steps:
1. Process audio files first – using Audition or Izotope
2. If I’m going to have to use camera audio at all – export it as a wav and again, process in Auditon and bring back to Premiere
3. Open Premiere, start a new project and place all the video and audio clips on the timeline.
4. Send to Plural Eyes by going to “Window””Extensions””Plural Eyes” and the Plural Eyes Window opens – then click “Synchronize”
Your method of syncing the better audio after synchronizing the video clips adds an unnecessary step and possibly some headaches as it’s my understanding that Plural Eyes needs to work with complete files, not edited pieces.