One day I will get around to writing up GBA sound hacking... I find it so tedious though.
Several of the tools you have seen for pokemon will also do for this, the sappy thing is good stuff. Fire emblem and golden sun hackers also use such things and have good info from time to time.http://www.romhacking.net/documents/462/
is a nice document on the format used by a lot of games on the GBA, there were several games using other formats though. Anyway that will cover editing in place,
If you want hardware and gbatek is not enough then http://belogic.com/gba/
(navigation at the top) is good stuff.
Many convert songs from midi into a format the GBA can take and call that the extent of their sound hacking. A bit ham fisted for my taste but to each their own. Alas a lot of the tutorials are very steeped in their methods rather than teaching you the underlying concepts so you can maybe break out of it a bit and get it done a slightly different way, and as such I am not sure what I want to link. Either way though the pointers to the song, the banks (instrument libraries) it uses and the actual song itself are all things that usually get changed here. Looping is nice but don't get too bogged down in it should you stumble across a tutorial.