What I did was download the newest r4 kernel (operating system) from the r4 website. Extract with winrar all files to the memory card. Make a new folder in the root called Game Roms. Drag and drop the .nds files into Game Rom folder. They will work from root but it just keeps everything tidier when you want to delete some games off in the future. Enjoy!
Make sure you leave a few Mb spare for the .sav files to be created (game save files) otherwise games will not run.