I prefer the white filing boxes. We currently are barely set up after moving schools so our system is just functional. Eventually I'll have us organized to:
(everything in alpha order, in its category.)
UIL - by grade and in alpha order
Solos filed in a filing cabinet by instrument and class. Class sets of books just organized in score order.
I do not recommend assigning a 'call number' to a piece if you're trying to stick to an alphabetized system just because it gets complicated when you add new tunes.
There is no wrong answer, though, since you need to build a system that works for your ease of use. Keep the end user in mind as you build.