Well, once you have the backup, you just need to restore it to work with cia format.
There is another app called JKSM. Its have a better interface, but at least for my experience, its not work with gateway. This is good only with you have a original game cartridge or cia games.
Just a brief explanation. Gateway will save each game in the root of the SD card. Something like XXXXXXXXXXXXXXXX.sav, where the Xs are the code of the game. But only gateway use this method, so its not compatible with CIAs, for example.
But, for SaveDataFiler, 000400000FF40A00 is the code (and always will be) of the cartridge. For example, if you put a original cartridge in the slot, SaveDataFiler will see this code as the save that is inside the cartridge.
Once you rename a save to 000400000FF40A00, you will be tricking SaveDataFiler saying that this is a save from the card, and than, you will be able to backup as a format that it could restore as a default format.