As @ut2k4master already stated, correct, for the time being, keep your EmuNAND on 6.2 if you still want to to boot into EmuNAND.So, double-checking:
I'm really new to the EmuNand method, installed it and is in 6.2, my SysNand is however in 7.0.0 for e-shop and online play. I can update my SysNand to 7.0.1 because it will not compromise the boot up or anything related to the EmuNand, is that it?
It's recommended that you use EmuNAND purely in OFFLINE mode to prevent BAN, nothing is 100% safe but being completely offline in EmuNAND will minimise the risk since your not connecting online in anyway.Seriously, from what I've been using lately, there is no point in running the TE's OS when you can run a EmuNand instead. I'm keeping the EmuNand in a different card, unless there's some system flagging method, I am assuming it's pretty much undetectable (assuming you're under the wi-fi safe mode in your emunand, nothing would ring more alarms than the same switch logging into Nintendo servers with two different firmwares).
Thanks Guys!
Use your Real NAND to go online, eShop, online gaming, I keep my EmuNAND on the same SD CARD, at the moment, from what I have read, Nintendo is not doing any file checking on the SD CARD to detect CFW/EmuNAND/Etc...
Even though EmuNAND has the ability to go online, it doesn't mean you should, as it will certainly raise some flags, the point of EmuNAND is to keep it separate from your Real NAND where you do all your dirty stuff, play XCI's, install NSP's and homebrew without touching your Real NAND.
At the end of day, your Switch, you do what you think it's best.