Ah, cool idea. In terms of tools for doing monophonic stuff...I guess you can use anything. That said, I found it to be rather easily doable with both PXTone and also with tracker software.
I would recommend you away from the stuff I did in my thread (which was rather experimental and practicey) and towards the music I did for my compo entry
which are a bit more musical (if you download the windows version, the tracker files should be in the XM directory).
I haven't played pokemon g/s/c. When you say you're going to compose themes, do you mean you're going to try and do monophonic transcriptions?
Anyway, do keep us updated on your progress
Also: "The 1-bit part of it comes in as I will be only using 1 instrument that plays 1 note at a time for all 8 pieces." <- Isn't technically true...the one-bit thing usually refers to the bitrate; I think
with 1-bit music you're essentially restricted to working with square waves of a fixed amplitude, and can only use a limited range of notes. Don't hold me to that though; I'm not too well versed on issues of bitrate and sound quality.