What do I copy my eMMC and dump my keys with ? With Hekate ?
copy the eMMC, yes with hekate payload.
(payload is a boot program you send to the console's RCM mode, using TegraRCM, or another RCM sending method).
dump the key with LockPick_RCM (another payload).
you can launch RCM payload with TegraRCM, or even whithin hekate.
I like to use Hekate as initial payload, it allows me to manage the console and SD content and partitions, and boot other payloads (lockpick, linux, android, Atmosphere, etc.)
sorry, I don't understand what you mean by "anything".
If you launch eMMC, you should be in official firmware, never run homebrew on that one (it's possible, like if you follow that youtube video you posted. but you shouldn't).
So, if you update eMMC, it means you update your official firmware using the official Nintendo's servers, or a game card, etc.
updating eMMC means updating your console officially. not "anything".
all the content of the emuMMC is separated from the eMMC.
you have different games, different savegames, different firmwares, etc.
if you want to update something on the emuMMC, you'll have to be more specific.
Oh, one thing I forgot to suggest, and that's one thing guides NEVER cover, the "after the hack" :
When you run emuMMC using Atmosphère for the first time, you might not see any differences from eMMC.
you don't know if you are running eMMC CFW, or emuMMC CFW. that would be bad if you start launching homebrew on the eMMC that you should keep clean.
they are both clones, so to be sure you are on the "emulated" one, located on the SD card, go to the console settings > console (at the bottom), and look at the firmware version.
13.2.0| AMS1.2.5|E <-- E here means emulated
once you'll have different content/games on that emuMMC, you'll see quickly if you are not on the correct one.
When you are on the Emulated MMC, remember that the "console memory" where you install your games is actually on the SD card's partition copy of the eMMC. not the real "console memory".
eMMC : console data = console chipset
eMMC : SD data : SD card's "nintendo" folder.
emuMMC : console data = emulated MMC partition on SD
emuMMC : SD data = SD card's "emummc/RAW1/Nintendo" folder
remember they are completely separated.
so if you had games installed on the "SD data" that you want to get back and play while on emuMMC CFW, copy the "nintendo" folder content into the "emummc/RAW1/Nintendo" folder.
you better have a big SD card
There is also another thing guides don't usually covers, is installing additional homebrew in the correct folders to make it more usable, or editing the settings before first use.
for example :
copy, rename and replace hekate payload (update.bin) into atmosphere's reboot_payload.bin
it will allow you to launch hekate directly from your console, no need to push it with an RCM dongle/windows/phone.
While on Hekate, you can eject the SD card without shutting down the console, put back the SD and launch AMS again. no RCMdongle or injector needed.
Copy atmosphère's fusee.bin into hekate's payload folder.
so now, you can launch Atmosphere from hekate using "payload" > "fusée".
or you can make a hekate ipl file to add atmosphere to the "launch" menu, pointing to the fusée file. additional boot method available from hekate (using fss0 instread of fusee.bin) allows you to boot eMMC with CFW even if you have emuMMC present (why would you want that?), or stock eMMC without any CFW patches.
copy lockpick_RCM.bin into hekate's payload folder, so it unlock the "get keys" menu inside hekate.
you can also launch it manually from the "payload" folder, but hekate has a dedicated option for that payload if present in that folder.
edit Atmosphère hosts/emummc.txt config files to filter nintendo's URLs when using emuMMC. (prevents you from playing online too! if you want to play online, there is another method to hide your consoleID instead)
edit atmosphère config to enable USB3 speed support for homebrew. (it caused issues when using file based emuMMC, so it's off by default).
No guide ever cover the different Atmosphère configs the user might want and their effect, or how to use them.
if you want to launch retail games you install yourself.
you need new patches for each new release of Atmosphère, check the "checkum" of the patch and AMS are matching. extract to SD root and overwrite.
I recommend using DBI homebrew to access your console and SD card content over USB MTP protocol on your computer, instead of shutting down and ejecting the SD card. preserve your SD card slot spring.
DBI also let you install games faster and easily, no worries about games bigger than 4GB to split on SD card, or having the wrong bit flag, or having twice the needed space available to install a game, etc.
you might want to look at a homebrew appstore.
let you browse and install homebrew directly from the console (you need internet access, so be sure you filter nintendo's urls first)
there are CFW updater homebrew you might find useful.
and finally, after all that explanation and help, here is a link to a guide :
and I found this one, modified to add things I said guides are missing (URL filters, hekate boot file, copy the nintendo folder, etc.) https://switch.hacked.us/