I assume that you mean BulletProof FTP Server and not client.
Yes, you can make a directory somewhere on your drive and put shortcuts in it to your other partitioions.
You then set BFTP to "follow" .lnk files in the user (or group options). Then set that directory as the user's HOME and give permision to read the other partitons.
You can also use a text file to set up symbolic links... but I have never done that.
Reply here if you cant find the options, I am not at the machine with my server, so I don't have the screens to look at.