How to Integrate custom JWT as Auth method for Atlas Device Sync

Im trying to connect my existing backend JWT (Laravel Sanctum) to a new Atlas Sync app.
My app works entirely with the JWT right now but i am trying to use the Custom JWT from atlas. Im not sure how to connect it.
In the settings I do not see a way to specify my server URL or the JWT generation URI.
In the docs you can see the user passes the credentials to the Realm App, in my case this s phone number and a one time code. Then realm Forwards credentials… but since i cant set up the URL how do i know where realm is sending these credentials ?
What am I missing here?