When numbers (00-05 or something) are in a file, is that what costume the changes will be applied to?
If so, is it ok for me to just change that number to choose what costume is overwritten?
Yes.
And what if the model also has move changes (psa I think it is?) Will the changes only apply to that costume?
PSAs affect all costumes for the character it's applied to. They cannot have numbers appended to them, and because of this they cannot be assigned to a specific costume.
What inserting things like songs, which (I believe) don't have locations to overwrite in the file? So far I've just been throwing mod files into my ssbb folder which knew where to change things, but how would I specify further?
To replace songs just rename it to the ID of the song you want to replace. Like say a song already in Brawl has the ID X05 (and there is), rename your custom .brstm to that ID (X05.brstm) and it'll replace that song.
A little bit on a tangent here, but does anyone know if any codes exist that I could plug into Riivolution to unlock everything in this game?
No I don't think there is any code to unlock everything in the game. Codes people develop for Brawl hacking are more towards affecting the gameplay or how certain things in Brawl appear or run. Unlocking everything in the game is more of a conventional cheat code Action Replay or GameShark would use, or one you would find on the internet by inputting various button combinations. The codes we use are more advanced.
Lastly, it seems like Riivolution only recognizes my ssbb folder every 3 or 4 times, and I'm always exiting and reloading. Anybody know what this is about?
You're saying Riivolution reads all your stuff fine, then when you exit and come back it doesn't? That makes no sense. Have you changed anything around before the time it stopped reading? Are you sure you have everything in the Riivo menu enabled and the correct codeset?