For firmware 19.x.x I'd stay on Atmosphere 1.8.0, provided that everything you usually do works fine without issues. I'm not sure if the way Atmosphere 1.9.0 or newer works (new helper module, memlet) has any significant impact if used on an older firmware, but as far as I know it should be backwards-compatible.
You can safely update Hekate and sys-patch. As far as I know you don't need to turn off custom theme unless you're installing different firmware. As for mistakes, if you haven't run into them, that should be your answer. The things that get changed are usually the things that aren't directly visible to the end user. You don't have to remove config files but it doesn't hurt either. I've never used AIO update app of any kind as I've preferred to do everything manually because that way you have a bit more control over what gets updated and what doesn't.
If your sysNAND is on the latest firmware, you'll definitely need to update your Atmosphere in order to do what you want to do.
