You can use your current setup of SX's Emunand (hidden partition on the SD) to boot Atmosphere's Emummc using this tutorial. This will be considered as dual emunand booting. Take advantage of the both worlds.

CLEAN UP SYSNAND
> Skip this step if you're using SX's Emunand and being online on Sysnand.
> If you didn't have any previous clean nand backup before
You have no choice here to clean up a dirty nand without a clean nand backup but to believe in this method
> Stop here if you don't want to hurt yourself or even me
Skip this step if your Switch is a brand new one or never ever been hacked.

Access NAND using PC

What you will need
- biskeydump
https://files.sshnuke.net/biskeydumpv8.zip
Run the payload and write down (or scan QRCode) Bis Key 2
BIS KEY 2 (crypt): NUMBERS
BIS KEY 2 (tweak): NUMBERS

- memloader
https://files.sshnuke.net/memloaderv2.zip
Copy *.* in [sample] folder to SD and plug it in the Switch
Run the payload [memloader.bin]
Unplug any USB cable
> Choose emmc line
> Plug USB C <> USB A cable to the Switch and PC

- HacDiskMount
https://files.sshnuke.net/HacDiskMount1055.zip
Run the tool under Administrator permission
> Open Physical Disk > Choose Linux line
> Double click on SYSTEM and fill BisKeys2 in the small table on top
Crysto > BIS KEY 2 (crypt): NUMBERS
Tweak > BIS KEY 2 (tweak): NUMBERS
> Press on [Test] > you will get OK! Entropy
> From Drive Letter table > Choose a drive disk, N for example.
> Press on [Mount]
Install driver if needed.
Acess N drive from My Computer
> access save folder
> delete all files inside the save folder except 8000000000000120
> Press on [Unmount]

> Double click on USER and fill BisKeys3 in the small table on top
Crysto > BIS KEY 3 (crypt): NUMBERS
Tweak > BIS KEY 3 (tweak): NUMBERS
> Press on [Test] > you will get OK! Entropy
> From Drive Letter table > Choose a drive disk, N for example.
> Press on [Mount]
Install driver if needed.
Acess N drive from My Computer and Delete Everything
> Press on [Unmount] and unplug the USB cable
> Press on [Power] button for 15s or so to reboot the system

> After rebooting, the system will be in initial setup stage.

CREATE EMUNAND AS HIDDEN PARTITION ON SD
> If you're SX Users and have been using their Emunand as hidden partition, just skip this step, go to COPY FILES
> Take advantage of SX Emunand creator (without valid license needed)
> Your SD will be formatted, backup your savedata and other data are needed.
Before creating emunand > Ensure you did delete all WIFI connections and turned on Airplane / Flight mode

Go to SX website > download their latest boot.dat > copy to the root of your SD
Download payload.bin for activating payload via your chosen tools

SX OS Bootloader Menu
> Options
> EmuNAND
> Create EmuNAND
> Hidden Partition on microSD

You will get "successfully done"

COPY FILES
Go to Atmosphere GitHub and download the latest release 0.9.0 and extract all files/ folders to the root of your SD

Create > emummc folder on the root of the SD

Create > emummc.ini file inside of emummc folder

Copy and paste this to emummc.ini

[emummc]
emummc_enabled = 1
emummc_sector = 0x2
emummc_nintendo_path = Emutendo <<< delete this line if you're not SX Users or don't want to keep using SX as your primary CFW

Hope this will help out.
Enjoy!