If there's no emunand partition on the SD card, it will actually run on the sysNAND, you just won't be able to tell unless you have a different theme or icon arrangement in sysNAND. However, installing a CIA to sysNAND is a risky move - if the install backfires, you run the chance of bricking. To differentiate emuNAND and sysNAND with a theme or icon placement is a good practice - it'll help you to identify what you're running and prevent accidental upgrading.
Are you sure there's no emuNAND partition on the SD card? If it's there, it'll boot into it no matter what. Completely format the SD card and try it again.
I formatted with windows default sd card formatter. Is there another program that I have to download? Or do I use Format emuNAND in Gateway menu?
Hm, then it should be running in sysNAND. It might be the 3ds preventing you from running it then. Format emuNAND in the GW menu sets up the emuNAND for you to use.
It might be my 3ds because when I enter Gateway mode and install a .cia file and turn my 3ds and turn it back the .cia file is not there.
