Updating Atmosphere is as easy as deleting the old /atmosphere folder and files then downloading the new ones from the official GitHub page. Updating the firmware is a little bit harder. You're on the right track since you used ChoiDujourNX but nowadays, everyone uses Daybreak which comes bundled with Atmosphere by default meaning you can find it in the /switch folder from the zip file that you downloaded from the GitHub in the last step.
Thanks! So using SDSetup is no longer used/recommended? I remember using it last time as it bundled a bunch of things together but not sure if there's any advantage over just getting atmosphere from the official repo