There's homebrew apps for the DS that allow you to restore/backup saves from DS carts. You'll most likely need a DS Lite to do this though There's a R4 brand USB save dongle thing that does this too, but I don't own one so can't say where to get it or how to use it. You can't run this kind of homebrew on the 3DS because you can't swap DS cartridges without the 3DS subsystem kicking you out with an error screen.
Depending on the emulator you played the game in, you "might" need to convert it to RAW format though. If it's some odd compressed format or some byteswapped order or other funky business that the emulator saved it in, you'll need to convert it first before saving it to the cartridge.
If you have access to a DS Lite and/or the USB device dongle thingy, the best route is to extract an existing save from the cartridge you want your pokemon on and using the Pokegen app (save game modifier for Gen 5 games) to transfer your pokemon from the emulator save file to the extracted save file from the cartridge, then rewriting it back to the cartridge. (you have to select all the pokemon in the box and "drag" them onto a folder location in Windows. It will save them all as PKM files. Then drag said PKM files back into the program into an empty box once you have the extracted game save file open in Pokegen)
I think Pokegen has better compatibility with other non standard save file standards used by emulators and would be less risky then trying to transfer a save file direct from an emulator into your cartridge.
But if you do know for a fact that the save file your emulator is using is compatible, then it's much quicker and you can just use the R4 save dongle thing or DS homebrew to write the save file to the official cartridge.
I had some Gen 3 pokemon I eventually got into a Black 2 game I played on a R4 flashcart. I know for a fact the save files can be written direct to an official cartridge since I had already done this with an official copy of Mario Kart DS. So I plan on buying Black 2 and then simply dumping the save file onto that cartridge using DS homebrew since I still own a DS lite. Then they are on their way into Pokemon Bank.
I might not get around to doing this till Alpha Sapphire comes out as I want to save the free 30 day Pokemon Bank trial so that I can do this with the latest Pokemon game.
