Advantages of fusee primary vs seconadry when booting Hekate to Atmosphere ?

Hekate has faster loading (by a few seconds) and can seamlessly switch between sysMMC and emuMMC. However, to support the latest firmware with atmosphere, I believe you need to wait for hekate to update (which isn't too long after atmosphere is updated). This is usually recommended one to use.

Fusee-primary focuses on one of the mentioned MMCs, and is a bit of a pain to swap (need to edit the emummc.ini file). Don't need to worry about this if you only need CFW on one of them.

 

Another thing that wasn't mentioned is that while there are no inherent differences to the boot methods aside from time spent booting, only one homebrew application out of all known homebrew apps will not work with fss0 and that is DZ. But there are plenty of alternative title installers so that is a non-issue.