You can still use the MMS for games, as the only difference is that there are a few tiny files in a 'ghost partition' on the stick. Personally, I prefer to reformat to normal. It's easy enough to make magic again at any time.
You can also use your MicroSDHC card for playing your games. The difference will just be that it will be slightly slower in the loading times. There are quite a few topics where people posted their speed results for comparing various MS and MicroSD card results. No matter which you use, it'll still be faster than loading from UMD. Just beware that a MicroSD card has a much shorter (i think it was something like 20%, off the top of my head) read-write lifespan than MS cards, due to the fact that it's so small (I've got 4, and the first 2 are already starting to go bad after 3/4 years but my 8GB MicroSDHC is still working great).
Also in my opinion, CFW is much, much better than using a flash cart, even considering the M3 Sakura's standard in flashware. I just wish that the same technique could be applied to other consoles than the PSP and PS2.
