Hi, I'm an owner of both a CycloDS Evolution and an EZ 3-in-1, and I can add a bit to how awesome it is.
With the Beta GBA support on the Evolution
(Beta GBA support on most recent full Evolution firmware,
and full GBA support on most recent Beta Evolution firmware) ha
There isn't any need to flash the games to the EZ 3-in-1, you can just play the roms straight through the gui of your Evolution, the same way you would load up a DS rom. In fact, it's recommended to do it this way so that the Evolution can properly keep track of your save files (it's better to use the save files stored on your SD card rather than the ones which are flashed to the 3-in-1). SO it's that way basically for management purposes and to prevent save files getting mixed up.