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.
Link farms should work fine. You should also be able to add multiple directories. Use the web interface to add multiple directories, or go into the config file directly and add multiple directories (comma separated) to the mp3_dir parameter.