Use GCC. It's available for 68k, WarpOS, PowerUP, MorphOS, AmigaOS4, AROS, etc...
About the platform... use the CybergraphX 3 API so it runs in AROS, MorphOS, 68k, P96 etc...
Do NOT use CGX4 functions!
For the GUI the best advice would be to use MUI (although I personally prefer Reaction) because it's available for OS3.x, AROS, MorphOS and OS4.
And simply use makefiles. Start with a 68k makefile and when everything works make some copies and modify them to compile ppc code...
