That is the issue with fusee and why I primarily dislike it. Fusee autoboots whatever is pre-configured in the BCT.ini file and you can only edit it on your computer. While you can modify Hekate's files from a computer, you can manage all of its options from within Hekate itself.
One of my boot options In hekate is fuse primary. But most of the time i skip hekate, It s an unnecesary extra step. I only have hekate set up because xecuter doesnt load fuse primary directly without hekate. when i use rcm loader everything is easyer .