1. I use KEGA fusion v3.51 (not sure what the latest is) running through Mala
2. I know it emulates alot of the consoles - I have Master System, Genesis, 32x, Game Gear (handheld), SG-1000 and SC-3000 (computer) all working with no problems. I never got the CD one working correctly and never got around to figuring it out but KEGA does emulate it I believe. I have no idea what a Master CD is but 32x was an upgrade to Genesis/Mega Drive but not many games were made, fewer than 10 I think.
3. after setting up KEGA, it uses command line options such as -32x, -gens or -gg to load the different systems, so set them up as different systems in your frontend (hyperspin) with different folders.