Here are all the steps for a Switch on 3.0.0 or lower (to prevent burning fuses, and hopefully not get banned using online (no Nintendo services).) going with atmosphere. You can also follow them using a switch on a higher firmware version, but I'll go through all the eventualities, in case people would want to downgrade later.
0. Disable automatic software updtes in the switch settings.
1. Put in the 90DNS, while still unmodified
https://gbatemp.net/threads/90dns-dns-server-for-blocking-all-nintendo-servers.516234/
2. Boot into Hekate (
https://gbatemp.net/threads/rcm-payload-hekate-ctcaer-mod.502604/) - use a guide for whatever method you are using to boot hekate (or any payload, hekate prefered, in rcm), while having a 32GB (or bigger) exfat formated sdcard inserted. Back up boot 0/1 and full nand then shut down again. (Hekate has its own exfat driver, no worries here if your switch firmware doesnt.)
3. Insert a fat32 (32k cluster size) formated sdcard (might need guiformat (
http://www.ridgecrop.demon.co.uk/index.htm?guiformat.htm) for bigger cards), with the following content on (= follow this guide):
https://switchguide.xyz/sdcard.html for atmosphere.
You could skip setting up checkpoint, hb-appstore, and sys-ftpd.kip (in fact, you probably should skip sys-ftpd - as it might have issues with newer atmosphere), as they are just optional "apps".
4. You probably will like to put these onto your sdcard as well (those are the sigpatches atmosphere doesnt come with on its own):
https://gbatemp.net/threads/i-heard-that-you-guys-need-some-sweet-patches-for-atmosphere.521164/
If you would like to be able to downgrade to 3.0.0 or lower some time in the future, make sure to use the nogc version and DONT SKIP THIS STEP.
5. Boot into Atmosphere for the first time (using hekate) to see that everything worked.
6. If you'd like to update your firmware - without burning more fuses, use
https://gbatemp.net/threads/choiduj...ller-homebrew-for-the-nintendo-switch.513416/ - and get the firmware packages from *cough* the tip in the first posting of the thread just linked. Make sure that autorcm is always enabled in choixdujournx, if you'd want to downgrade at all in the future.
Thats it. No intermediate sdcard "all in one zip packages", everything from its source thread. All eventualities accounted for.
Tested up to 6.1.0. (by me personally only up to 6.0.1).
7. One more step. Get tinfoil, probably from one of those "all in one zip packages".
(
https://gbatemp.net/threads/newest-hekate-sdfiles-zip.506280/). With tinfoil you install (game) .nsp's.
Most homebrew software comes as .nro those get started via hbmenu - that gets started, when you enter the gallery while on a CFW. In atmosphere, if you hold R1 while entering the gallery, you'll actually enter the gallery for gallery stuff.
.nro's can be placed in the /switch folder or in subfolders in the /switch folder on your sdcard. subsubfolders are also a possibility.
Info for people wanting to keep the downgrade option open. If you are at or below 3.0.0 and want to keep a downgrade option to that open, make sure that the switch is ALWAYS on autorcm once you've installed a higher firmware with choixdejournx (choixdujournx will enable it by default - and its usually a one time thing until you down- or upgrade. If you make sure to only upgrade with choixdujournx - autorcm will be enabled again, by default. Just make sure you dont disable autorcm via hekate without giving it the longest of thoughts. One normal boot on a higher firmware = fuses fried.). and make sure you copied over the nogc patches (which will disable your gamecard slot - so it doesnt get a "higher than 3.0.0" gamecardslot firmware update).
The firmware on your switch will always be an "official firmware" - but it never will be booted into. The only way you boot is through hekate into atmosphere. Atmosphere will patch the official firmware "on the fly" to become CFW. This paragraph is only here so you dont get confused what firmware you are updating. (Always an official firmware through choixdujournx.) Updating atmosphere is simply done by replacing a few files on the sdcard. Always make sure you have the "sweet patches/nogc patches" in the atmosphere folder after updating (as they reside in one of those folders).
You can install the Joycon firmware update - IF you dont have modded joycons. If you also use your joycons as a jig - dont't update the joycon firmware - or read up on where to solder in a resistor before updating.
fat32 is used on your "daily use card" because it has proven to have less issues with file system corruption, should something go wrong. Because of that there is an extra step, when installing BIG(er than 4GB) nsps. Either use tinfoil usb transfer, or use this program:
https://gbatemp.net/threads/legal-nsp-splitter-for-fat32.520213/ (you also might want to use this program, in general:
https://gbatemp.net/threads/official-4nxci-a-tool-for-converting-xci-to-nsp.515341/ to convert xcis to nsps.)
Autorcm will not let you turn your switch on without injecting a payload over the usb port. The switch will simply "always" boot into rcm mode (black screen, looks like its turned off) - even without a jig inserted.
You also probably should buy one of those:
https://www.aliexpress.com/wholesale?SearchText=ns+atmosphere for ease of use.
Thats all.
One more ease of life edit: Use this version of ftpd (if you need an ftp program on switch, to later on transfer files back and forth):
https://gbatemp.net/threads/ftp-application.506434/page-5#post-8095478
edit: Went over it three times, didnt forget anything - this is a complete guide. Without relying on prepackaged packages. So you learn what stuff is used for what.