Apple Music (Media) Consolidation of files

Files are in multiple locations (physically as in external drives, folder structure outside of Music app) and want to consolidate these into the Apple Music file structure. Most all of the files currently work in the Music app, but need the external drive plugged in to play. So it seems the Music Library file is doing it's job well. What I'd like to do is take all these different locations: organize them into one physical disk without ending up with lots of issues (exclamation, greyed out, DUPLICATES, non-synced files) that can happen with lots of files moving around. Are there any tricks to avoid mess - or just use "Keep Media Files organized" in Music Settings. Thanks so much for sharing your expertise and experience.