One thing you can do is to check the Album Artist tag on these files. If they are correct, you can use Rename, Move, Copy Files (in the Library tools menu) to move the files to the location of:
[Album Artist]/[Album]
Currently, the problem is that the songs are in the default [Artist]/[Album], and if there is more than one artist on any one album it's going into multiple artists.
I should add that you may want to wait for another, more experienced, Music user to confirm the above. I use MC mostly for video, so my large music collection is somewhat of a mess itself.