The .0 file stores your main save. The others are for extra saves if a game doesn't have enough save slots. You can switch saves by pressing select in the G6 menu. The .is0, .is1 and .is2 files are real time saves for GBA games.
The .0 file is the only one you absolutely need.
One more thing you need to know is that after starting/playing a game you have to boot up into the G6 menu and let it process the save data before backing up or restoring a save file. If you don't, your backup will not be your most recent save or your restore will be overwritten.