this IS possible, I've done it with phantasy star zero because that game only allows 3 save slots. All you have to do is make a copy of the rom, then rename the second gta file something different. Such as add a 1 to it or something. Then when you save during that second game you have, the .sav on your sd should look like this- grand theft auto chinatown wars1.sav- or whatever you decide to add to the name of the second rom. Thus, you will have something looking like this on your sd root..................
grand theft auto chinatown wars.nds
grand theft auto chinatown wars.sav
grand theft auto chinatown wars1.nds
grand theft auto chinatown wars1.sav
it shouldn't create an issue if you us an AR code either because the game ID should be the same even with the name changed.
Hope this works if not message me and I'll help you get it working. Good luck.