All right, well, I went in there and tinkered around, got a ROM loaded and runnin', and was immediately reminded of why I ditched playing emulators through this thing. Make sure you "Load Core" before rummaging for the ROM. Here are the steps/folders/directories that worked for me:
Load Core > (Select an appropriate Core/Emulator, and then wait 3 years for it to load and kick you back to the menu) > Load Content > sdmc:/ > roms > (Select folder and appropriate ROM, wait another 3 years for it to run)
(And then delete all the stupid .cia/apps it creates on your home menu for each individual core for no good reason.)
If it's still not reading any ROMs, there's a chance that maybe your ROM folder is in the wrong directory or something. Make sure it's in "sdmc:/".
I highly recommend downloading and familiarizing yourself with the "New Super Ultimate Injector" for GBA & SNES games on 3DS, and avoiding this slow, clunky, crappy program entirely.