Updating isn't that hard, just update your hekate+atmosphere while you download the firmware package + extract to SD + install with daybreak. As long as you have sys-patch then you should not need to worry about sigpatches.
As a rule I just check which firmware is required by the games/updates/DLC I'm trying to play (with NX Game Info or similar) and only update to that exact firmware, since the latest is usually not the best.
If it doesn't boot after updating, delete your sd:\atmosphere\contents. This is the only part that can be a little annoying, because some of these files come with homebrew which needs them to work, but the files aren't labeled in any way. So you have to go through and update all your homebrew, tesla overlays, sysmodules etc. to ensure everything works after deleting the folder. Possibly some of them are not compatible with that firmware, or you have to look for workarounds/forks to get them working again. It can be a good rule of thumb to always delete this folder when updating but personally I only bother if there are crashes.
In addition to all of that, you should of course keep your homebrew up to date with hb-appstore to ensure proper functionality, especially when updating firmware or Atmosphere. This is a quick and painless process though.
In particular I believe EdiZon and many overclocking tools are incompatible with newer firmwares, but there are alternatives if you use those.
I tend to avoid installing sysmodules as much as possible, because they tend to break with updates, if there's anything you aren't actively using then you may as well remove it.
