So if I got you right, you don't use an emuNAND at all but switch between CFW (SX OS in your case) and stock FW only on your sysNAND?
In this case there's really not much you have to do. All your savegames are there. You literally just boot with Atmosphère into that very same sysNAND instead of doing it with SX OS.
If you use a CFW on your sysNAND you
can get hit by a ban wave
anytime. I hope you're aware of that.
After that being said, the easiest way for you would be to do the following:
- Download this very nice homebrew (as it does almost everything for you automatically) to your SD card and launch it from within SX OS using the hbmenu (not the SX OS rommenu) by holding R and launching any game:
https://gbatemp.net/threads/aio-swi...w-and-cheats-directly-from-the-switch.574043/
- There you do the following:
Download the latest sigpatches (you can just get both versions -> hekate and fusee),
download Atmosphère and say yes when it asks you if you want hekate too (to get you into sysNAND in case you want to).
- From your PC get the latest fusee-primary.bin payload (google for Github atmosphere, go to releases and there it is) and use that to boot into Atmosphère or use the hekate payload (google for hekate ctcaer github) and use that to have a bootmenu that lets you choose what to boot.
- Optional: Download FW 12.0.0 too from within the AiO Switch Updater and install it from within Atmosphère using the homebrew Daybreak (automatically comes with Atmosphère).
Let me know if something's not clear to you.