While you're unlinking NANDs, there's no risk of updating. You only have to format sysNAND, which will not require you to update. You may be prompted to connect to the internet, but it will not prompt you to update.
The only risk of updating sysNAND is if you don't verify that you're in emuNAND before you update; which is the same risk as using a 3DS flashcart.
It's very simple to install cias once you're finished. Just place the cia on the root of your SD card and use one of the cia managers to install it.
Thanks for this. I'll run before I can walk though! I will follow the tutorial and then I'm sure I'll be able to work out when I'm in emunand using the Gateway files as the FW letters have a pre(suf)fix anyway. Thank you again, I'm sure it's annoying when someone is asking mundane questions that everyone in the scene already knows! I am pretty computer savvy so let's give it a go!