Are you using the SD Media Launcher? It sounds like you're using something similar to it, anyway, one helpful homebrew program I personally recommend is GCMM (GameCube Memory Manager); I originally had this on my Wii, then I eventually got it working with my GameCube. It allows you to backup the entire memory card or any individual game's save(s) to the SD card, and it can also put new saves on the memory card that are on the SD card (for this, I find it's easiest to put individual saves on the memory card, even if they overwrite a previous save file for the same game). It's helpful if you play a game on the Dolphin emulator, and want to use a save from your memory card.