Basically, get hekate
https://github.com/CTCaer/hekate/releases
Copy the bootloader folder on sd, and instead of booting fusee.bin with picofly, boot the hekate payload, it will generate default config file
Then in hekate, go to tools, usb tools, and press sd card. Connect your switch to your computer with the usb cable, and at sd:/bootloader/hekate_ipl.ini, add something like this:
[Atmosphere]
fss0=atmosphere/package3
If you use emummc, then add
emummcforce=1
If you need signature patches, get the patches.ini file from the signature patches and place it in the bootloader folder, and add
kip1patch=nosigchk
So it would look like this:
[Atmosphere]
fss0=atmosphere/package3
emummcforce=1
kip1patch=nosigchk
Then go back to the hekate main page, the first icon on the left (dont remember what it's called), and you can select your Atmosphere boot entry