What you see in the interface is different from the file structure.
In principle it is not related to the folder structure at all.
In the interface tracks are considered to be an album if the “Album” and the “Album Artist” are the same. That is the default and a very common convention.
If you think of titles like “Their greatest Hits” or “Beethoven symphony no.5” you understand why.
As MusicBee is very flexible, in Preferences > Sorting > Grouping you can change this.
You might even decide to use the Folder as a grouping criteria but I do think using tags instead of a folder structure is the way to go.
My preferences is to keep the tracks of a CD or download together in one folder.
Hence I have
AlbumXXX\CD1\
AlbumXXX\CD2\
Within each folder each track (filename) is prefixed with the track
01-title a
02-title b
I do so because sometimes a track is missing.
If this is due to wrong tagging, having all the tracks in 1 folder and having them sorted by track number makes it easy to locate this missing track physically and re-tag.
Having the above mentioned folder structure, you still can display a multi disc set as one by using the tags as the criteria for grouping.