This is my first tutorial post so please tell me how I can improve. I figured out how to do this when I thought to myself "You can have multiple emunands per partition on the 3ds. Is there a way to do it on the Switch?" As it turns out, there is. Keep in mind that this tutorial uses Ubuntu, not Windows or Mac OS. Also keep in mind that my sd is 512GB. This even lets you have more than 3 partition based emuMMC's.

What you need:

• Hackable Switch
• Sd with a capacity of at least 128GB
• ReiNX toolkit
• Atmosphère's hid-mitm (if you're on 9.0.0 or above)
• Ubuntu
• gparted
• USB sd card reader (Ubuntu's drivers for sd card slots aren't very reliable)
• A lot of free space on your computer

Let's get started!

Step 1: Dumping nand or emuMMC
Use ReiNX toolkit if you want to back up your emuMMC or Hekate if you're backing up your sysnand. YOU HAVE TO DUMP BOTH RAWNAND AND BOOT0/BOOT1!
Step 2: Preparing the images for flashing
Type in this command on your computer:
cat /path/to/boot0 /path/to/boot1 /path/to/rawnand > emummc.bin
THE ORDER MATTERS! If your rawnand is in parts, put their paths in order by number. This will create a file in your home folder called emummc.bin.
Step 3: Repeat steps 1-2 using a different file name in the cat command until you have as many files as emuMMC's you want.
Step 4: Preparing the SD card for flashing
Open gparted. Shrink the FAT32 partition on your SD to a size where it'll leave 29828MB times the number of emuMMC's you want of unallocated space. Then, create a partition from that unallocated space (The file system doesn't matter).
Step 5: combining the images
Type this command:
cat /path/to/each of your nand images > emummc_combined.bin
This will take a long time to complete!
Step 6: Flashing
Go into gparted, disks or anything that shows the location of your sd partitions in /dev. look for the partition you made in step 4 and remember the thing that looks like /dev/sdXX. It'll most likely be /dev/sdb2 if your sd is the only external storage plugged into your computer. It might not be /dev/sdb2 though.
Type this command:
sudo dd if=/path/to/emummc_combined.bin of=/dev/sdb2
replace sdb2 with whatever you saw earlier. This will ask for an admin password. It won't show as you type it and that's normal! This will take a long time to complete!
Step 7: Creating configs
Create a folder on the root of your sd called something like emunand configs. Create folders within there for each of your emummc's. Open gparted. Right click on the emummc partition and choose information. Copy and paste the first sector into a decimal to hex converter. You can find one by Google searching. Open text editor and create a file with these contents:

Code:

[emummc]
enabled=1
sector=0xwhat you got in the decimal to hex converter
path=whatever you want as long as all emummc's have something different
nintendo_path=whatever you want as long as all emummc's have something different

Save to one of your emunand config folders as emummc.ini.
Repeat the process adding 61087744 to the the previous first sector used in decimal and converting that to hex and using that in the file and saving the file to a different folder. Put one of your emummc.ini files into the emummc folder.
You can switch emummc's using NX-Shell to replace emummc.ini in the emummc folder with a different emummc.ini. ​

There, you now have multiple emummc's on the same partition and can have more than 3 of them!