On my fileserver, I had my music laid out across several drives and under several folders as well.
What I did was use a program called “Winbolic Link” (google it) to create “symbolic links” underneath a single folder. If you’re familiar with *nix or BSD you’ll know what symbolic links are.
By doing this, you’re effectively linking the contents of the linked folders to their original locations, while appearing as though they are underneath the folder they are linked to.
It works extremely well. I recommend it.