Just chiming in on my experience, since I was too was wondering this a while ago and there wasn't any info about this setup, only snippets of info here and there which I didn't get my answer.
Yes this is all obvious for most, but for others that might just getting on board the EmuNAND train, it might not be so obvious.
For those who are on the fence of getting a hackable Switch or who already has one and would like to use EmuNAND.
For me, when EmuNAND was an option to be stored on the SD CARD (Before EmuNAND had an options to be as a hidden partition):
- Factory reset OFW to start on a clean slate.
- When the Switch shuts down, I boot into SXOS boot loader and made a EmuNAND on SD CARD (also applies to hidden partition EmuNAND).
- Booted into OFW and setup the Switch as per normal until I got to the home menu.
- Booted into EmuNAND and setup the Switch as per normal until I got to the home menu.
- In EmuNAND, enabled FLIGHT mode and turned Controller Connection (Bluetooth) and NFC to ON.
- Changed the Themes to Basic Black, so OFW is on Basic White and EmuNAND on Basic Black, I do this so I know if I'm on OFW or EmuNAND, very handy.
- Then continue to setup/customise both the OFW and EmuNAND.
Now you have:
OFW: Use this for online stuff, games, eshop, etc...
EmuNAND: This is where you do ALL your dirty stuff offline, stay off grid.
Since I only got the Switch recently and since the EmuNAND on SD CARD is kind of new (not talking about Hidden Partition EmuNAND here), I have been online in OFW to grab YouTube and Fortnite, booting up legit Splatoons 2 cart and doing online game update and installing eShop demos. Have not been banned yet, touch wood, but I might have a high chance of not being banned, since, as for as the Switch and Nintendo servers are concerned, it doesn't know anything about EmuNAND.
For those that don't know, when you create a EmuNAND as a Hidden Partition, that 30gb or so of space allocated on the SD CARD, this is not wasted space, this is your EmuNAND, feel free to install games/game updates to this NAND, as this is NOT your OFW NAND, but your EmuNAND, they are separate to your SYSTEM NAND.
I found that my 125GB card will filling quickly so I got myself a 400GB card, since I've already made the jump to the hidden partition EmuNAND, there was no easy way to migrate the hidden partition to the new card, there is a way of using the dd app, there is a post on GBATemp about it and how to do it.
Since I didn't want to factory reset my OFW and go through the above again, this time around I just setup EnuNAND as a hidden partition again, for those that don't know, yes it does make a CLONE of your OFW, so MAKE SURE you enable FLIGHT mode because when creating a EmuNAND, so you don't want to accidentally go online when you boot into EmuNAND.
When you boot into your EmuNAND, just do a factory reset within EmuNAND and your good to go, you'll have a fresh EmuNAND to start over.
This is good for that that don't want to do a factory reset of their OFW.
Hope this little info will help others.
Added Notes:
Just to add, before I did any of this, my OFW has been legit, meaning I never used CFW, never launched any homebrew stuff or installed NSP's, etc... So if you have messed around with your OFW and also went online with CFW, etc.. then you may have already been flagged for ban at some point so use at own risk. Again, if you have a clean system, then you may/might/could have a higher chance of not being banned.
