Very Important to do your Nand backup before you do CFW. More info at Making Nand backup with Hekate tool
If you want to run clean Atmosphere
follow these steps
1. Make sure your SD is formatted to fat32
2. Delete EVERYTHING except the folder named "Nintendo"
3. download the latest Atmosphere zip file and extract to SD card https://github.com/Atmosphere-NX/Atmosphere/releases
4. download fusee-primary.bin, this is the payload you will use to boot your Switch. (It will go in your tegrarcumgui, on your dongle, on your phone)
5. download Sigpatches from here and extract to SD
6. when in RCM, inject fusee-primary.bin
7. Hold R while tapping the Album Icon to enter the Homebrew Menu.