The Music app never picked up on where I had them and imported my songs on its own. I had to import all of my music into the new Music app again. It processed the files and then copied them to the new location. Don't be surprised if you see another folder created when it does this. I ended up with /Music/Music/Media/Music after it was finished copying everything. But it's working now so I'm just gonna leave it where it is.
Edit: I should mention that I did that several times and it didn't work. I ended up finding a tweet where a guy said to delete everything from your /username/Music folder AND deleting all folders with a reference to "iTunes" or "Music" from your ~/Library folder. Be sure to look in the ~/Library/Caches folder as well. Delete that stuff, reboot, put your music back into the /username/Music/Music/Media folder (or wherever you like), and try importing your library again. Since I did this, Music has worked as expected.
Thanks a lot for the tip! And I wasn't able to get around to this until late last night so hence the late reply.
But all of my music are in iCloud library, so I basically took your advice, but instead of importing tracks locally, all I really had to do was wipe out my downloads, then redownload the tracks again. Music then files it in the correct spot.
I do have some local stuff in my iTunes library that isn't music that I had to manually import though, and that are music videos (not purchased from iTunes or added from Apple Music), iTunes LPs, and PDF booklets. I am deleting the music videos and re-importing those now without any problems. iTunes LP imports are also fine and load just as they used to in iTunes
But I'm having issues with PDF booklets. They just get reinserted into your library under "Unknown Album" and doesn't file properly back in to the original album they belong in. They also don't load at all if you double click them so I guess PDF booklets no longer have a place in your music library? Other than this though, I'm able to get everything else back in so I'm pretty happy about that. I did submit a bug to Apple though about Music not automatically organizing and consolidating your library as it's supposed to, so hopefully this gets resolved super quickly in the next few weeks.