I’d keep the organization if I were you! You can configure beets to sort things into top-level folders if you like. Take a look at the paths section of the configuration—you can automatically tell soundtracks to go in the Soundtracks directory, for instance.
I have managed to make some progress with this and so far loving it! I think I have the organization sorted into those three categories, only 2 things I cannot work out at the moment is why it is encoding mp3’s? I only want it to encode lossless files to mp3. I thought these arguments would skip encoding any mp3’s 320 or less? and why it is leaving the original files? I have it set to move
plugins: fetchart embedart convert scrub replaygain lastgenre chroma web discogs
directory: /music
library: /config/musiclibrary.blb
art_filename: folder
threaded: yes
original_date: no
per_disc_numbering: no