For GBA games you have a *.sav file for each game, which has the same filename (just like you suggested in your example). For instance, if you have a rom named mmzero_02.gba, when you run the game through the GameManager to put the rom onto the SD card (it's easier to use the program than to do it yourself), it'll automatically create a save file for it in the "GAMESAVE" folder (which it will also create in the root of your SD card).
For DS games, it's pretty much exactly the same, except the save file is put into the NDSSAVE folder with the extension *.dat (but otherwise has the same filename as the DS rom you're playing).
What you're saying you want to do is take your saves from your GBA, DS, and SNES carts and put them onto your flashcart so you can continue your progress. This is possible to do with a DS game (on your DS, you can use your flashcart to take the savefile off a normal DS game), but for a GBA and SNES game, that'd require more work, and you'd need to build/buy a rom-ripper. For the SNES game, to apply the save file to the SNES emulator.. I don't think that's even possible. Sorry.
Good luck. Hope this helped. ^^
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