Using the API.
The endpoint https://example.com/notifications?username=Falco which can be discovered using How to reverse engineer the Discourse API and navigating to a user profile Notification page.
You will need to pass an Admin API Key to be able to query notifications from any user.
Depends on your app.
A good default is:
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When you are rendering a new page in your main app, you will know your current user.
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Translate your app user id to a Discourse user id (and cache this for a long period)
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Query the notifications endpoint in Discourse (cache for a short period)
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Render your app page with the Discourse Notifications
For Dismissing, a click to dismiss will need to hit your backend and then you issue a PUT to https:/example.com/notifications/mark-read. That needs to clear your app notifications cache for the user.
Advanced stuff would include listening to new notifications in a Discourse plugin (or a PR to core that adds a Notification webhook. That would allow your main app to keep an websocket or server-sent events and update notifications in real time.