1) Is there anything I should not do besides update emunand to 9.6 and enter data management on sysnand?
The most important thing to do is stay on 9.0 in sysNAND, that means you should know exactly when you're in sysNAND and when you're in emuNAND, for example when you're in emuNAND if you go to System Settings and then close System Settings you will be booted back into sysNAND, so it's important to know that. Some big games like Monster Hunter 4 kicked me out of emuNAND when I closed them on Old 3DS, not sure if that's the case on New 3DS, but the point is when you unlink your emuNAND from your sysNAND, create one folder in your sysNAND named "S" (or you can go as far as creating a bunch of folders that spell "S" "Y" "S" "N" "A" "N" "D"), this is an indicator that you're in sysNAND, and you can also create a folder "E" in emuNAND (or a few folders that spell "E" "M" "U" "N" "A" "N" "D") to indicate that you're in emuNAND, this way even if you get kicked out of emuNAND for whatever reason you will always know that you're in sysNAND and should not update under any circumstances.
Everything else to be honest is not such a big deal, because whatever you do in emuNAND can be undone, worst case scenario, you can re-inject your old emuNAND, or if you don't have a back-up of your emuNAND, you can format again to wipe your emuNAND, so whatever happens in emuNAND is not a problem.
2) Regarding unlinking sysnand and emunand, is this basically how I should do it: Format Emunand (to install it for the 1st time), backup sysnand and emunand, take out internal memory card and format sysnand (to unlink), then upgrade emunand (via a game like Xeno)?
I would suggest you to use 3DNUS
https://gbatemp.net/threads/3dnus.376488/ to update your emuNAND to 9.5.0-23.
It's really easy to use.