It's getting asked a lot which method to update your Switch or which version to update, so I will try to cover these questions. This guide will (hopefully) be updated with new firmware when they come out.
WARNING 1: I do not take responsibility if you damage your Switch.
WARNING 2: ChoiDojourNX has a higher chance to brick your Switch! It's especially not recommended to update Sysnand with it!
NOTE: This guide is compatible with all Switch versions (Unpatched, Erista Patched, Mariko, Lite).

1. Which Version To Update?
1.1 Updating SysNAND:
If you are updating your sysNAND, than you are probably doing this because either you are going to play online or download a game that is compatible with newer firmware. If you are updating SysNAND because you don't have an emuNAND, then create an emuNAND and update that.
If you are still here then you need to update to the latest fw. DO NOT UPDATE RIGHT NOW IF YOU ARE USING SX OS!

1.2 Updating EmuNAND:
You can update to fw 12.0.1 if you are using Atmosphere. SX OS DOESN'T WORK ON RECENT FIRMWARES.

2. How to Update Your Switch?
2.1 Updating SysNAND:
Step 1: Update your cfw (and Hekate) to the latest version.
Step 2: Create a backup of your SysNAND! You can do it from Hekate or SX Boot Menu. Make sure to keep your backup in a safe place.
Step 3: You can update to the latest fw by official method, if you can't update your switch with the official method then you should use Daybreak for Atmosphere (comes pre-installed ) and (See Part 2.2, Steps 2-4). Note that, updating with the official method is safer.

2.2 Updating EmuNAND:
Step 1: Update your cfw (and Hekate) to the latest version.
Step 2: Get your fw files and copy them to your Switch's sd card in an extracted way.
Step 3: Decide which Updater to use; Daybreak for Atmosphere(comes pre-installed) and ChoiDujourNX for other cfws. If you will use ChoiDujourNX then download it to your switch from here.
Step 4: Open your updater from HB and follow the given instructions. It shouldn't become enabled but still make sure that AUTO RCM IS DISABLED if you are using a patched switch during setup!

DONE! Now you have successfully updated your Switch!

If your Switch crashes during boot and you have installed a custom theme before then try deleting the /titles/0100000000001000 and/or /titles/0100000000000811 folders from sd card.

If you have a fw 11.0.1 SysNAND and you are using SX OS than DO NOT downgrade. Instead switch to Atmosphere.

 

[masagrator]

every homebrew title isn't supported in fw 10.2.0

What?

And most importantly - don't ever recommend ChoiDojourNX. Ever. It has bugs that may hardbrick your modchipped Switch when updating to one of newest FWs.

For Atmosphere - Daybreak.
Dunno what's the best solution for SX OS now.

 

[GCS]

What?

And most importantly - don't ever recommend ChoiDojourNX. Ever. It has bugs that may brick your modchipped Switch when updating to one of newest FWs.

For Atmosphere - Daybreak.
Dunno what's the best solution for SX OS now.

You are right, most of the hb titles are supported aren't they
If I know correctly Daybreak isn't compatible with SX OS. I recommended ChoiDojourNX because Xecutor said that they fixed the issues with ChoiDojourNX. But I am gonna add a Warning part about that. Thank you for your recommendation.

 

[masagrator]

You are right, most of the hb titles are supported aren't they
If I know correctly Daybreak isn't compatible with SX OS. I recommended ChoiDojourNX because Xecutor said that they fixed the issues with ChoiDojourNX. But I am gonna add a Warning part about that. Thank you for your recommendation.

They didn't fix the core issue with ChoiDojourNX because it's closed sourced. This bug occurs in all Switches randomly, but in modchipped it may result in hardbrick because of no access to RCM. They fixed bug that was in SX OS which was triggered by ChoiDojourNX.

 

[GCS]

They didn't fix the core issue with ChoiDojourNX because it's closed sourced. This bug occurs in all Switches randomly, but in modchipped it may result in hardbrick because of no access to RCM. They fixed bug that was in SX OS which was triggered by ChoiDojourNX.

If you update emuMMC with ChoiDojourNX, and your emuMMC gets "bricked?". Would this effect the whole system too?

 

[masagrator]

If you update emuMMC with ChoiDojourNX, and your emuMMC gets "bricked?". Would this effect the whole system too?

Updating emunand won't brick Switch if SX emunand implementation is good. If emummc/emunand gets bricked, you can always make new one.

 

[n0k0m3]

If I'm updating SysNAND using official method booting from Hekate with AutoRCM on, will this burn my fuses?

 

[GCS]

If I'm updating SysNAND using official method booting from Hekate with AutoRCM on, will this burn my fuses?

I don't think it will cause a problem, but if you are really worried then you can close AutoRCM and open it after the update (Not sure about this' effect)

 

[n0k0m3]

I don't think it will cause a problem, but if you are really worried then you can close AutoRCM and open it after the update.

Also another question, so I'm having both SysNAND (OFW not modified) and EmuNAND (CFW Atmos 0.14.4) at 10.1. Can I update SysNAND to 10.2 while keeping EmuNAND at 10.1? (I know it's a bit of a weird question since ppl usually do the other way around)

 

[GCS]

Also another question, so I'm having both SysNAND (OFW not modified) and EmuNAND (CFW Atmos 0.14.4) at 10.1. Can I update SysNAND to 10.2 while keeping EmuNAND at 10.1? (I know it's a bit of a weird question since ppl usually do the other way around)

You can do that. You don't need to update emuNAND if you don't want to do so.

 

[Deleted member 540526]

nice

 

[Corpus99x]

I want to update the fw on my emuNAND, do I also need to update the fw on sysNAND or can they be on different versions? (emuNAND will be 11.0.1 but sysNAND would be 10.2.0)

 

[GCS]

I want to update the fw on my emuNAND, do I also need to update the fw on sysNAND or can they be on different versions? (emuNAND will be 11.0.1 but sysNAND would be 10.2.0)

They can be in different versions. (If you are using SX OS note that fw 11.0.1 is not supported.)

 

[Corpus99x]

They can be in different versions. (If you are using SX OS note that fw 11.0.1 is not supported.)

Thank you!

 

[Corpus99x]

I updated emuNAND to 11.0.1 using daybreak on atmosphere 0.17.1 (hekate is 5.5.2) but now when I try to run a software it comes up with "Could not start the software". My SD is FAT32.
Is there an easy way to solve this or will I have to format everything and restore a backup?

--------------------- MERGED ---------------------------

I found a solution (in case anyone else has same issue)
Using AIO switch updater download sigpatches
Restart the system, enter RCM, inject payload, boot atmosphere