Damn. I tried running Omega Ruby and it's just black screen. Is it easy to use emunand? I don't wanna mess things up.
Also, are there issues with using microSD as FAT32 and not exfat? Which do you prefer?
There are no issues with FAT32 vs exfat. Just you will have to use Gateway's rom splitter for anything over 4GB on fat32. Don't think there are any games over than size yet anyway.
Emunand is easy enough to use.
Copy everything off your main SD (the one in the 3ds).
Grab Gateway's latest launcher and put that on the SD.
Hold L on boot. If you haven't already, use the NAND backup option (this is just a precaution and should be done even if not using emunand), then once it's done, copy the backup to pc and safely store it.
Hold L on boot again and use the format emunand option.
Boot into Gateway mode, go into system settings, make sure it says GW3D before your version number.
Use the system update from within system settings and it will update emunand to latest version.
Once emunand is up and running, just copy everything from your sd card back (except for the old launcher.dat)
Gateway will automatically boot emunand if it's present. Also do not go into system settings, then back out. That drops you back to system nand and has resulted in people updating that and not emunand. Go into settings, check it says GW3D and use the update function, do leave the settings inbetween.