All of the gba releases that use flash save types are here
http://releases.pocketheaven.com/asearch/?...ase&=Search
These are the only gba roms you must patch, via the HW1 patch when writing the rom to your microsd "to ensure that each game saves properly".
All games not on this list should work without any patching (HW2 patch option).
(Manual HW2 Method)
If you don't want to use the m3 game manager for non flash save type gba roms, use this method.
Copy the gba rom into the root of your microsd card. Use the bank.dat file found in C:\Program Files\M3 GAME Manager\gamesave .
Just rename "bank" as the same title of your rom, and place in the GAMESAVE folder on your microsd card.
You can boot the M3 Lite into DS mode via your R4 or Cyclo DS using the 3rd icon of either carts main menu.
At the DS menu press start to go to the GBA menu. "You need to do this in order to play your gba games."
I assume you have the m3 lite for gba purposes as you already own two very nice flashcarts.
I myself have never dealt with the nds portion of the m3 perfect, and only use it for gba games.
You made a good choice!
Have fun with the M3!