this is a GREAT question. I’m going to have @jeremiah answer this, since he can answer it authoritatively.
The matching rules are broken into two phases. The first clumps the files into albums, the second actually identifies.
For clumping, the best you can do is put 1 album in 1 subdirectory, and have media number and track number fields completely filled out in the metadata, with no missing tracks. Contiguously numbered tracks in a subdir with no other files will always get clumped together. There are many other cases for clumping, but this one will result in the best result.
WIthout a good clump, you will have a hard time getting a match.
@jeremiah will talk more about this, but I think putting the discs themselves in different directories would probably lead to less errors as well (both by the clumping algorithm and by you). Be sure the tags have proper media number tags!