https://gbatemp.net/threads/when-to-use-fusee-primary-vs-fusee-secondary.573484/

• Hekate → Fusee-Primary→ Fusee-Secondary
• Fusee-Primary → Fusee-Secondary
• Hekate→ Fusee-Secondary

• Send Payload “Fusee-primary.bin” > boot Atmosphere (fusée-secondary)
• Send Payload “Hekate” > chain-boot fusee-primary.bin > boot Atmosphere (payload=)
• Send Payload “Hekate” > Hekate uses fusee-secondary to boot Atmosphere (fss0=)

• Hekate (and Nyx interface of Hekate) set by Kosmos ready-to-use package lets you choose how you want to boot your console (Stock, SysMMC or emuMMC) directly from its menu. But this choice can only be applied if you launch Atmosphère with fusée-secondary (“fss0=”).

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.

• Using fss0= with fusée-secondary potentially allows for the following boot modes directly from Hekate:

Stock-like sysMMC sysCFW emuCFW This increased flexibility, all in one menu would not be possible if booting using fusée-primary.bin

• These are atmosphere sigpatches, not fss0, so they require using fusee primary (directly or through hekate) to work.
• The patches you linked are for Fusee Primary, off course it ain't going to work without fusee primary.bin. If you want to to boot using fusee-secondary, you have to use Fss0 patches.
• …

• fss0=fusée-secondary
• payload=fusée-primary

• primary/atmosphere/*.ips
• secondary/atmo+boot/*.ips+.ini