I use Windows Explorer, right click on the external drive folder where the FLACs are stored, drag cursor to the My Music folder (in the Music library) and then create a shortcut there. For example I have music stored in the folder FLAC Music 1 on external drive H-the shortcut is: "H:\FLAC Music 1"
I just create a new shortcut in My Music for every "FLAC Music XX" folder I have on an external. In the FLAC Music XX folder I create subfolders for each artist, then subfolders for each album under that (for compilation albums I put them in a subfolder Various Artists). The nice thing about this system is no matter how many artists or albums I add under FLAC Music XX they will show up automatically in My Music (of course, if using slimserver you have to rescan your library there to bring it current).
If you look in my "My Music" folder all you'll see is a couple of shortcuts.