A couple months back I posted a little note about how to get nested audio into Soundtrack Pro from FCP and I have a better method that is surefire and doesn't take much longer. You can bring this into play at any point along the workflow but at the start is the best so you dont have to even think about how it might effect edits.
This all works whether you are syncing with Pluraleyes or doing it manually with a slate and is pretty easy.
1. I've found depending on your time and computer speed you can either a) batch convert into Prores ahead of time/on import or you can wait until you sync.
2. Sync your timelines up with Pluraleyes or by hand. One thing, if its interview footage, that can save you time and give you a little boost in logging better is to group takes into single timelines. Make sure your timelines all match with the correct codec you are using for your workflow, i.e. Prores HQ 1920x1080
3. Here's really the last step already, select all the timelines you have created and set them up with Media Manager to render out. I use referenced Quicktime clips so I dont need to rerender everything.
4. Reimport all the new clips you just created and you're ready for editing. If you decide to do this as a later step, for instance, if you are nesting sequences, you can drill down to the timeline you need to condense and media manage it into a referenced clip.
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