Help with merged clip decision for a short film

Greetings and thanks in advance for any perspective you can offer.
I've begun to edit a short film (10 minutes) that has 3 hours of dailies.  The clips are all merged clips, created with dual system audio and synced with Plural Eyes 3.
However, before setting to what's sure to be months of work, I wonder if there was a better workflow.  Bear with me.  To begin with, marker comments do not stick with merged clips.  As soon as you select another clip - poof!  They're gone.  And there are other limitations that may or may not affect me down the road.  I guess I'm saying I'm not completely sure what I might want or need to do at some point, but I'm concerned that I'll be limited for using merged clips.
I've realized I can use Plural Eyes to merge my clips and audio fully outside of Premiere CC.  Those clips, once imported, retain marker comments and suffer no other "unique" limitations.
It will be a massive undertaking to resync, re-import, and retag and organize everything - but perhaps in the long haul this is prudent?  Or not?
I'm cutting with Prores 422 at full size 4K, so replacing media isn't a concern.  Anything else I should be worried about?  There's always a chance I'll use a 3rd party to color-correct with a DaVinci.
Thanks again.

I shoot for about -6dB, with no peaks above 0dB.
Sounds like you have a very weak signal. I'd set away from PrPro and handle this in SB, or Audition. Listen carefully with a good pair of noise-canceling headphones first, and then test on monitors.
Are you working in mono, stereo or 5.1 SS?
Good luck,
Hunt

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