So you could start your clean nand backup (using the hekate payload that you just updated, 4.6). Atmosphere itself goes onto your SD card. You could use hekate to launch fusee-primary too. Hekate supports chainloading other payloads. You could use fusee-primary to boot Atmosphere. There's also USER1, USER2 and USER3 provided for you to customize it with 3 different things.
You could put anything payload on any directory. The name of the directories are there as a reference. Your payload injector supports multiple payloads.
