For anyone reading this now, I recently struggled with the same problem.

Flow

Here is a simple process:

• Create shopify remix app following the steps in the official docs. This will be the app that the store owner will install on their stores
• When the store owner installs the app, from remix app you can easily access the offline access token.
• If you want to do API calls within this remix app then you don't need to do anything extra because all auth is handled in the template itself.
• If you want to run some tasks in the background like a cron-job then you need to authenticate your node (backend) app. For this you need the access token from remix app to get data about the shop directly from your backend (Node app in this case).
• You can send the access token to your custom backend and store it in a db.
• Since the token that remix app created by default is offline access token it will stay valid until the user uninstalls the app.

How to get the access token from remix app (made from official template)

const { admin, session } = await authenticate.admin(request);
console.log(session);

This code is provided in the official docs Here you can console the session and get the access_token from it

This can be a little confusing for anyone new trying out. But I hope this helps!