In the same situation here. (going from SX to Atmosphere on unpatched Erista switch v 11.0.0, using SX os jig/dongle to boot into CFW) I followed this guide at it worked great:
https://rentry.co/SwitchHackingIsEasy
I formatted my SD card, created an emunand, confirmed Atmosphere is on it and copied back my original SD card backup files.
My only issue is when I power on the switch, and use the jig/dongle, it ALWAYS boots into SX OS sysnand.
If I hold + i can get into SX os boot menu. (I don't want SX anymore, just like the jig/dongle so I don't need to use Tegra RCA on my PC)
If I go click CFW on the main SX OS boot menu, it boots up SX sysnand. If I go into SX menu options, I can manually select the hekate ctcaer payload, which will then bring up that blue screen with the 'launch' and emmmc and other tools and such. Clicking launch, I can then select Atmosphere and it boots into Atmos emunnand fine after like 20 seconds.
But this pathing seems so unnecessary and time consuming. I watched a video where a guy setup Atmos using a jig/dongle and it would boot straight into atmosphere, or give him a direct choice if he held + down and would let him go to emunand atmos or sysnand easily.
What am I doing wrong? Ideally I would like to have the switch autoboot into Atmosphere everytime when the jib/dongle is connected and switch powered on. If I update emunand Atmosphere to 12.1 using Daybreak, will that mess anything up?