If you have a custom theme installed, make sure to uninstall it before you proceed to update.
You can backup your saves with JKSV and restore them after the update should you need it.
Usually, you should update Hekate and Atmosphere first, followed by sigpatches. Always check the which is the latest supported official firmware.
Once you do that, update firmware via Daybreak as well. You can find firmware files on that certain site we aren't allowed to link to (that's what I usually do) or you can dump the latest firmware if you update your OFW.
If you used either Haku33, TegraExplorer, EmmcHaccGen or ChoiDujour in the past, you might run into a
save issue after updating to 17.0.0 or newer. To fix it, make sure to boot at least once into sysNAND CFW with Atmosphere 1.6.1 or newer.
If you've used Incognito_RCM or similar in the past in order to blank your prodinfo, Atmosphere will crash as soon as your console connects to the Internet and tries to connect to the Nintendo servers due to your console not having valid prod keys.
You won't run into this issue if you are always in airplane mode or if you're using
DNS MITM.
If you plan on connecting your console to the Internet, you can use
this patch and/or DNS MITM.
I guess I've covered everything for now.