I love apple, but font book is pitiful as a font manager. as far as using it to clean up,
you can deactivate sets or individual fonts you don't want active, then restart. also, fonts are kept 3 places:
mac hd>library>fonts, mac hd>system>library>fonts, and mac hd>users>your username> library>fonts. you can delete unwanted fonts from the first and last ones, but the system fonts have to stay, and some fonts that are basic like myriad, arial, etc that you may find in the other 2 are installed and used by some apps, so leave those basic ones.