You need to load the kernel onto the microsd card via the adapter b4 any games will work, heres the most uptodate one if you don't allready have it..
Go to the R4 site and grab the (latest is 1.10 as of this post) kernel:
R4,R4DS kernel Downloads-Revolution for DS-NDS,NDSL,Flashcart,CleanROM
The ZIP file will have an "English" directory: inside of "English" you'll find "moonshl" "_system_" as directories and "_DS_MENU.DAT" "_DS_MSHL.nds" as files.
Those two directories and two files (and their contents!) should be placed in the root of your flash card.
...and that's it. You can place your clean, unmodified backups in the root directory and away you go.
I've still not zipped my games up yet so i'll go and find some links where to download them from.