Add the kip1 patch under the launch options for CFW. Here is an example.
{--- Custom Firmware ---}
[CFW (SYSNAND)]
emummc_force_disable=1
fss0=atmosphere/fusee-secondary.bin
kip1patch=nosigchk
atmosphere=1
logopath=bootloader/bootlogo.bmp
icon=bootloader/res/icon_payload.bmp
{}
[CFW (EMUMMC)]
fss0=atmosphere/fusee-secondary.bin
kip1patch=nosigchk
atmosphere=1
logopath=bootloader/bootlogo.bmp
icon=bootloader/res/icon_payload.bmp
{}
Make sure the SD card is FAT32.
Remove all CFW files/folders from your SD card (that would be folders like /sept/ and /atmosphere/)
Download the latest Atmosphere
Download the latest fusee-primary (next to Atmosphere)
Download these signature patches (for Atmosphere v0.13.0)
Put Atmosphere and the signature patches onto your SD card
Put the SD into your Switch
Enter RCM
Launch Atmosphere using fusee-primary