I'm open to suggestions.
Until now no limit has been reported to how large a library MusicBee is able to handle.
So for that matter one installation of MusicBee should suffice.
But, if I am reading into your situation correctly, I think I would suggest using two portable installs.
The first one where you just load everything into that you have.
It might be messy, but it's a starting point, and it will show everything you have, including all 'problematic' files that you will need to address. You can check them for tags, albumart, genres, etc.
Also it will allow you to test and learn settings and preferences for MusicBee that are important to you.
Then, for all albums/recordings that you have processed to your satisfaction, move them to another folder/drive that is managed by the second MusicBee (portable) installation.
So that folder/drive will now hold your cleaned-up music library, and it should also be a more stable MusicBee setup because of what you have learned from testing things on the first installation.
The second installation will easily handle all your files, and since the tags for the files should now be in order, allow for any kind of managing and filtering.
On a side note, personally I do have two portable installation these days for a different reason.
I have one for classical music, and one for non-classical music.
The reason for that is that there are a couple of essential differences between the two genres that became too tiresome for me to try combining in one setup comfortably.
Also I ran out of available custom tags to accommodate for both genres, and having two installs solved that for me too.
But for a library only containing non-classical music I see no good reasons for splitting things up.