I have a quite a bit of experience with music libraries and also hold an Masters of Library and Info Sciences.

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.)
Holiday
UIL - by grade and in alpha order
Marches
Pop/Fun music
Sight Reading

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.