your dilemna sounds like what i'm experimenting with now. i am using real-world GIS data, and then transforming it into fictional space with gimp.
you can load in country/continent polygons, then reshape them with the tools available in the GIS software.
then i paint over, re-surface, re-texturize until it looks nothing like the original landform...adding water bodies, new mountains, flora, etc in gimp.
still new to me though, working on some projects now, will post in future when possible.