Google for Game Genie or PAR codes to defeat the region lock (and any other cheats you want at the same time), then use the cheat manager in the menu (or you could also pre-patch the rom using something like ucon64 for things like the region code so you don't have to set it in the menu every time).
EDIT: The cheat manager isn't available to flash-only carts in the current menu. I should probably change that. I guess Conle only allowed cheats with the SD because you can save the cheats to the SD card. He probably figured people didn't want to type cheats in every time with the rom. So for flash-only carts, right now you need to pre-patch the roms before burning. I'll do some tests about getting that in the menu.