Efficient Way to Edit with Secondary/Independent Audio?

Hello community,
I do a lot of documentary package work and I've finally gotten fed up enough with my workflow to ask this question.  Is it possible to efficiently edit in Premiere Pro when your primary source of audio is independent of your video?
For example I have an hour's worth of audio from an independent audio recorder.  I sync multiple video clips up to the audio using PluralEyes.  Then I import that XML into PP-CC.
From there I have an hour long sequence where I mute all but the independent audio track.  And when my producer gives me a script that says to use the SOT from Clip 06: 01:23;01 - 02:01;00,  I have to find Clip 06 in the "good audio" sequence timeline, then double click on it to bring it up in the source window, then put the timecode in the source window, set an in point so I have a reference in the sequence with the good sound, then note the sequence timecode so that I can use it when I put the sequence in the source window so that I can finally get it into my package sequence.
And after dropping a few different sequences worth of SOTs, PP takes forever to "Prepare the Audio."
For instance, I'm currently looking at Media Encoder for a minute long package which it telling me it's "Preparing Audio (40 or 517)".  It will take a few hours to prepare that audio, then minutes to render.
I know I've got to be doing something, or perhaps many things wrong.  Can anyone help my workflow?

Anyone have an answer to this?

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