Hey @nickblue
I recently just went through the same process seemed to have figured it out, so hopefully this might be able to help if you still needed it.
One thing out the gate to note is if your app contains the remix template for the admin portal this won't be hosted by Shopify, from my understanding it's because the admin renders in an iFrame which needs an external host, so you'll need to create your app with no template and only with the extension you want, which I'm assuming you did based of what you said earlier, but figured I'd mention it just in case.
After you've created the app, and tested it you then run npm run deploy to release the latest version. After this you'll go into your partner dashboard, into your app, and under distribution create a custom app install link for the store or organization that will use it. After this you'll take the link and install it on the store, and then you'll need to go into the stores settings under Checkout, click Customize Checkout and under the app embed section in the customizer make sure your custom app is selected. This should allow your app to then be present and running within checkout.
This was the process I ran through, and where everything seems to be working. I hope this helps in some way, good luck!
