Because I'm new to all this, please excuse my lack of the correct terminology. I'll explain this the best I can. I haven't been on my switch for a long time. I booted my switch up normally and updated it to 10.0.3. Took my SD card out and completely wiped it. Moved the required Atmosphere and Hekate files to my SD. Created my partition, created my emuMMC, booted into CFW emuMMC. Got to my homescreen, went to Album to see the apps I had on my SD. Updated Pokemon by Options/Software Update/Via internet. I never installed anything or ran Goldleaf, or tinfoil. I did use Checkpoint, but that's it.
Edit: bit more detail.