Got it to work after a few tries, had to restart the Vita at least once.
File transfer worked well using Filezilla (had an old version, so I updated it). Drag and drop.
Tried the Mega Drive emu. Speed is excellent (@444mhz), sound needs work. Looks good and crisp @ 2x native res. Doesn't seem to be any way to enable 6-button controller configuration (that I could see).
Followed up with the SNES emu, but couldn't find the roms I transferred over. They were all zipped, so maybe the emu can't see them. I'll unzip 'em and try again later.