I am not quite sure of what you are asking.
The only way you can save is saving as you would do on an actual DS, so making a regular ingame save. That file is then what will be loaded every time you load the game (with the correct savetype). If you want to load another save (like say you are playing the game on your DS at the same time, or you want to load a friend's savegame or something like that) then you will have to make sure it's a RAW save (for instance a special flash cart save like the R4 has will not work without first being converted or something like that (not too sure on the details)) and then you will have to place the save in the battery folder inside the no$gba directory and rename it ot exactly what the name of the DS game file is (so if you have PokemonPearl.nds then you have to name your savefile PokemonPearl.sav when you place it in the battery folder).
Also as a tip before you start playing rename all your games so that there are no special characters in the name, or any spaces or pretty much anything, just letters, this is because occasionaly a special character may cause problems when saving, as in the game does not get saved correctly.
I also suggest you check out questions 8 to 10 in my FAQ, perhaps the answers there will clarify things a little more.