So you can do this on Atmosphere 0.9.2 EmuMMC.
Initially you should have a clean NAND backup (i.e. Pre-hacks and CFW/Homebrew if you don't ...shame on you for skipping that step!). Save it in safe place(s).
Hack your switch as you see fit (I just used Kosmos). Once you are happy with things....(you can install games later I suppose).
Install Renix. I move the sept folder temporarily for atmosphere to sept_2 or whatever. Boot into Renix and run incognito. This makes a prodinfo backup - save this too (your NAND backup has this safe technically but never hurts to have this too!).
You should have your SDCard partitioned to Fat32 how you like it. I took a 256GB card and made two partitions. The first MasterBoot record at 221ish (named it EmuMMC) and 33GBish for 2nd partition Fat32 (named it NAND for my NAND cuz I am using 1 sdcard for Emunand and Nand...might not be smart but oh well for now I'm not going online yet...hehe). Don't use GPT - It doesn't work.
Now I rebooted in to Hekate 5.x and used their EmuMMC tool to create a Partition Based EmuMMC (cuz file based is slow as ballz). Here it should detect the partition and let you install it.
You should note in the EmuMMC mount (after it's done and you activate it), where you should have your Ninten folder for your previously installed games/saves/etc. I recommend using a Windows machine to copy these. My OSx and Linux machines struggled viewing both partitions. If you don't use Winblows - your results may vary...
Now boot into CFW with EmuMMC and tada. You have Incognito'd EmuMMC. If you are all set and happy - You should be able to restore your NAND backup to the Switch and have a "Clean" NAND for going online.
Having EmuMMC with Incognito enabled will let you go online safely (as far as we know) and use HomeBrew APP store and other online network features (ProFTPd, lan-mitm,etc).
Thank you for sharing Blawar!
NOTE 1 - You should NEVER boot into CFW with your NAND as it can leave traces of CFW modifications it would seem. If you accidentally do this...you should restore a NAND backup if you want to be as safe as possible. To avoid this pain in the arse - I use Hekate auto-boot for CFW w/ EmuNand. If I want to use NAND, I just turn it on as normal (vs going through RCM).
NOTE 2 - Some people suggest using a 2nd SDCard for your Clean NAND setup (not having any CFW/Homebrew files on the card)...This might be the safest way to go...who knows.
NOTE 3 - You may still get banned - we're not sure if this prevents the ban but it's certainly our best shot so far!
NOTE 4 - I heard a "Brazilian" cat was able to unban consoles. I would assume he likely takes this tool and restores the prodinfo from a non-banned key to a banned console. This would require another switch's keys...and I'm not sure if this works (haven't tested - just theory here)... I did read elsewhere that someone tried and it didn't work...perhaps there's another step (or more) that needs to be taken... At any rate - Love this
NOTE 5 - Would LOVE to see this as a default feature (optional if we must) in CFW like Atmosphere/Kosmos, Renix, etc. SXOS has stealth mode so I dunno what that does...but they may not need/want it...whatever.