Migrate from SXOS to Atmosphere

You cannot just copy boot file into the SD card. There are a few important things you need to know to get this to work:
1-You need to install Atmosphere, not just the boot file
2-If you're using SX dongle to boot into SXOS, and want to use the SX dongle to boot into Atmosphere, you'll need to install Hekate
There's a guide, which I followed: http://3dsflashcarts2dsxl.blogspot.com/2019/07/guidehow-to-migrate-from-sx-os-to.html.
It sounds like you've been using SX CFW without emuNAND. Once you get this working, I would use Hekate to create a emcNAND and run off of that. On my Switch, I left all the SXOS stuff in my SD card so that I can boot either into SX or into Hekate/Atmosphere.

 

It's not my guide. I used that guide to install Atmosphere on my Switch. Good luck.

 

Use TinWoo Installer.

 

You can use USB in supported homebrews (but no XCI loading obviously)
I prefer to install games from my PC using USB or network rather than from an USB drive. It saves a copying step. Pretty much every title manager supports that, I use Awoo Installer with NS-usbloader.

 

I also use Awoo installer/NS-USBLoader over a network connection as well. That' has worked out well; no need to remove the uSD card or "plug in" anything else.