Download newest firmware here: http://gbatemp.net/index.php?showtopic=89197 Put the system folder you get from there in the root of your microSD. Put your NDS roms in a folder named NDS in the root of your microSD. If you have the ram expansion and want to play GBA games then put the GBA roms in a folder named GBA in the root of your microSD. Put the microSD in the M3 Real. Put the M3 Real in your DS. Enjoy.
Only two other things to remember 1) No more than 127 roms in a folder (make more folders if you need them) 2) Leave at least 1MB of free space per rom to create the save files etc (if you are going to use Real Time Save then it need to be nearer 2.5MB per rom)