Just have to make sure you downloaded the same version of fusee.bin as Atmosphere (they are in the same set of GitHub assets, right next to each other) and put it in /bootloader/payloads/ directory.Yes I have setup exosphere.ini and default.txt.
My hekate_ipl.ini:
[config]
autoboot=0
autoboot_list=0
bootwait=3
backlight=100
autohosoff=0
autonogc=1
updater2p=0
bootprotect=0
[Atmosphere CFW]
payload=bootloader/payloads/fusee.bin
icon=bootloader/res/icon_payload.bmp
[Stock SysNAND]
fss0=atmosphere/package3
stock=1
emummc_force_disable=1
icon=bootloader/res/icon_switch.bmp
…also since you have the protection set up please select stock Sysnand option in Hekate launcher during boot up.