http://www.reddit.com/r/musichoarder is a community of folks who are interested in that problem of organizing large amounts of music.

As for me, I'll download like 80 gigs of music, mostly playlists off qobuz, then match it all with albums and tag it using musicbrainz picard, then dedupe it against my collection with dupeguru, then normalize the volume using rsgain. I use Logitech Meda Server to play them. I rate songs with a star rating, with the RatingsLight LMS plugin. I listen to all my unrated songs on shuffle, rate them and put them in playlists. I'll listen to playlists based on mood, genre, country, or star rating. I have various bash scripts to process playlists.

It's really manual. If i wanted to, I could throw everything in the same playlist when i download a big tranche of music of the same type. Another neat tool is soundiiz, which enables one to move playlists between spotify, qobuz, deezer, and m3us. So you could export a playlist out of spotify, import it to qobuz, run qobuz-dl against it, and add all your new flacs to your local copy of the playlist. Soundiiz is the only thing i had to pay for, $4.

My music server's on a pcie ssd so operations don't take too long. I have a backup on a NAS and I mailed a second backup to a friend. Between me and my girlfriend we have 2tb of music.

I name files ~/Music/MyMusic/artist/album/track number - track title.flac I have playlists at the root directory with relative paths, so it's intact copying to a Digital audio player. I convert everything to Opus to fit a copy on my phone.