Your application can require merchants to specify their shipping account details, package size and any other user preferences you may require.
Set up a new tab in Ecwid Control Panel, which will serve as a settings page for your users. This tab will load a page from your server in an iframe in a separate tab of Ecwid Control Panel. See Native Applications
When merchant is in the settings tab of your app, your code can create and modify the merchant settings using the Application storage feature. It's a simple
When customer is at checkout, Ecwid will send app storage data in a POST request to your application URL alongside order details. The request will contain all data from your application storage, including public and other keys that were specified. Use it to identify the store and a user for the shipping rates.
After you get a request from Ecwid, your application endpoint should get its components and return correct shipping rates back to the customer in a response.