https://gbatemp.net/threads/when-to-use-fusee-primary-vs-fusee-secondary.573484/
If you have an emuMMC folder or partition and use fusée-primary (“payload=”) method to boot your console, Atmosphère will always follow its own setting to determine whether to use sysMMC or emuMMC regardless of the user choice in Hekate. While an alternative may be to edit Atmosphere config files to force disable emuMMC and reboot the console, the typical method is to edit “emummc/emummc.ini” and set emummc!enabled=0 or 1. 0 means disabled. 1 Means enabled. You can edit the file yourself, or use existing homebrew directly from your Homebrew Launcher menu, such as emuMMC Toggler or EmuMmcConfig and reboot the payload (fusée-primary).If you use Hekate, you could name your boot choice “Atmosphere” only.
Stock-like sysMMC sysCFW emuCFW This increased flexibility, all in one menu would not be possible if booting using fusée-primary.bin