The same way you originally made one. And if your goal is to have the save data on your emuMMC, then keeping the first one doesn't serve you any purpose so might as well delete it to regain that space.
This is a summary of what I've done
I have hacked my switch, injected hekate and did a backup nand and created emunand.
i wanted to receive save file from a different switch of mine. I was on 3MUMMC and I tried doing it and it wouldn't work.First of all, it asked me to go online and turn off airplane mode, and secondly i needed to have same nintendo user on both switches if i were to transfer save file. I had a different user logged in to my hacked switch.
i turned the switch off and turned it on as normal, without rcm, and created the same user, from the other switch, on the hacked switch. And i received the save file on the hacked switch, it went through, however it connected to nintendo. Then i turned it off and started hekate and launched emunand.
i was worried, my profile wasn't there and the game save wasn't there. You said emummc is a copy of my sysnand. And i created a new profile user after creating emummc.
after i created a new user on the switch, i should have created an emummc again instead of receiving save file and using checkpoint and transferring it over to another switch.
Because i was on sysnand and received save file from a different switch, i went on checkpoint and backed up a pokemon save file and edited it and restored it. Then i transferred it over to my other switch.
Will i have to do a restore of my nand and follow the step by step noob guide all over again?
Or should i create emummc again so this time my profile will be reflected on the emummc?
I've already connected to nintendo online by receiving save file and sending save file back to my original switch.
I did it once and i realised i might have messed up. I don't want to get blocked.
I hope you can help me out. I only used checkpoint to edit a pokemom sword save file and checkpoint is all i have in my album.
I hope you understand what i have done
Please help me mate if you can.
Thank you