I did this a while back and it took a bit to figure out since I didn't know what to do.
Basically what you need to do, is figure out what Atmosphere-specific files to delete - if you have any custom game patches or modules.
Then delete any installed custom Atmosphere modules, because those can cause crashing when upgraded (specifically MissionControl).
Otherwise you can almost delete the atmosphere folder - but don't, because there is a certain config file you need, lest you want to regenerate it (don't remember the name, but you can figure it out on your own I'm pretty sure.)
Do the usual Atmosphere install.
After all that, you can pretty much just upgrade the firmware in sysMMC using whatever method you like. Just to point out, if you're using emuMMC - DO NOT UPGRADE USING ONLY emuMMC. Use sysMMC first - it's less of a headache and you shouldn't completely brick if you manage to fuck something up.
This would be the time to install any custom modules.
Let us know if you run into any issues or are confused about something.
