Don't just assemble your .s file without first finding ample free space (you can get Free Space Finder here:
http://www.romhacking.net/utilities/540/). I usually set the search for bytes to around 10000 to be safe, and start searching at offset 700000 (I use FireRed, you didn't specify your ROM of choice which makes it harder for me to help you). I also don't directly assemble the .s file to my final ROM, I make a copy and use that as a dummy to work all the bugs out of my song, then export the tracks and import them into my final ROM.
To repoint your song to a safe offset, search for a lot of free space, copy the offset that Free Space Finder brings up, then paste that into the "first track" offset when importing the tracks.
For editing instruments, are you using the modded Sappy 2006? It has a very handy dandy Edit Voicegroup feature which you can use to fix your instruments. Be aware of the GBA's sound limitations, though: 5 DirectSound/Multi-sample tracks playing a single note (multiple notes and they will start overriding each other), Square Wave 1, Square Wave 2, Wave Memory, and Noise can all play at a time. This means you can have up to 9 tracks playing at once, but a maximum of 10 can be in a song if you need that, just not all 10 playing at once.
You will have to edit any MIDI not already tailor-made for the GBA in a MIDI editor, or else your MIDI will surely sound messy; I use Anvil Studio (a quick google search will work for that, it's free software but has a bit of a learning curve). I generally follow the rule of thumb that with chords (multiple notes which play at the exact same time), always keep the highest note. You may want to use the "merge" feature to combine redundant tracks of the same instrument, but always use "repair track" after doing this to fix any bad programming that merging tracks may introduce. In Anvil Studio you can edit the volume of the tracks, but I prefer doing this out of the .s file (there's a VOL line of code which corresponds to the volume, don't go higher than 127 on this!).
There is a complete instrument patch for FireRed, as well as a High Quality sound patch (both are in the Research and Development board), the latter of which reduces noise output (the noise may also be from your song being too quiet or loud; if it's too loud the song generates noise). The instrument patch was also ported to Emerald, I do believe. Don't bother with Ruby, Sapphire or LeafGreen. Ruby and Sapphire don't have very many instrument samples to work with, and all three of those ROMs have very little research compared to FR and EM. Also, here's a voicegroup offset reference for FireRed you may find useful if that's the game you are working with, and you don't want to use the instrument patch:
http://www.pokecommunity.com/showthread.php?t=148811 It doesn't have every instrument ever, but there are a lot to work with. (I personally have problems with the sound patch so I manually imported instrument samples from Fire Emblem games to fill in what I was missing and needed.)
I suggest getting the hang of Anvil Studio's learning curve, merging and simplifying music tracks, optimizing the volume for the GBA, and also program changes, which can be used to change a track's instrument and is easy to insert in Anvil Studio (insert > MIDI control event > program change...). Music hacking is hard, there's no getting around this. This is my field of expertise, so if you get stuck feel free to message me and I'll help you.
