bootloaderfolder to the root of your SD card.
Step 1. Download
hekate_ipl.ini from here and place the file in your
Atmosphere CFW uses the
fusee-primary.bin payload to load into atmosphere. Without disabling your emuMMC (if you use it), it will always try to boot your emuMMC with the sigpatches provided in the earlier steps of this guide.
Atmosphere FSS0 SYS uses Hekate's fss0 booting to boot your sysMMC (the NAND in your switch.) This won't let you launch game dumps, or homebrew like tinfoil due to how it loads. This option should mainly be used for dumping your own games on your internal NAND if you want to install them to emu later. Or for booting your sys in CFW so you can play Nintendo Online (not recommended this way, but should be fine if nothing "dirty" is done, IE, installing game dumps.)
"Stock" SYS boots your switch in "stock" OFW mode. I consider this not true stock as you're still using atmosphere to boot your switch. Many members in the Nintendo Homebrew discord say this is safe, but you're still relying on something else to boot your clean system NAND. I strongly recommend if you want to boot stock, disable AutoRCM (if you have it enabled), and boot without a payload at all.
Step 2. Copy
fusee-primary.bin to your SD Card in
\bootloader\payloads\ (grab it from here if you don't have it.)
Step 3. Rename
reboot_payload.bin and paste it in the
atmosphere folder. Hit yes if prompted to overwrite (this will allow you to get to the Hekate screen when you reboot your switch running CFW.)
Step 1. Boot into Hekate by injecting
hekate_ctcaer_X.X.X.bin as your payload.
Step 2. Select
emuMMC by tapping on it.
Step 3. Select
Change emuMMC by tapping on it.
Step 4. Select
Disable by tapping on it.
Step 5. Close out of the
Change emuMMC page and navigate back to the
Home page in Hekate. You can now head over to launch and launch your sysCFW.