Oh, cool! I have a basic idea for how to distribute them, just off the top of my head.

Cities: There will be one person in each city that will give you the music if you speak to them. Nice because it encourages players to talk to everyone and therefore fully experience each city.
Routes: Pokemarts could sell a few of the tracks for the music of routes near the city the mart is in, or they could be given by the guard dudes in those gate things as a welcome to the next area.
Caves and Dungeons: In pokeballs deep inside them. You might have to return later with new HMs to reach them.
Special Tracks-
Rocket Battle Theme: Given by Giovanni after Jirachi quest if Rocket, given by Simon at Victory Road if Orion.
Orion Battle Theme: Given by Ophelia after Jirachi quest if Orion, given by Simon at Victory Road if Rocket.
Gym Battle Theme: Given by that annoying guy who stands by the pillar and advises you after you obtain Sphinx Badge.
Elite Four Battle Theme: Given by Tristan (4th E4 guy) After you beat him.
Champion Battle Theme: Given by The Champion after you beat him.
Pokemon Center Theme: Given by Nurse the first time you visit a Pokemon Center.
Pokemart Theme: Given by Clerk after you visit a mart for the first time.
Bicycle Theme: Given by some dude near the Bike Shop, or however you end up getting the bike.
Topaz Main Theme (Do we have a main theme?): available at start.

Probably a couple others should be available to begin with, and again, this is just off the top my head, so we'll see if it's good or not.