I still don't see my question answered, however I could just be having a dense moment.
I have a Store, but it is not linked to any Partner (although, I do have one - I never associated my Store to my Partner account).
I have a very basic app - it simply has "Admin Links" - no other endpoints. All I want to do is to expose our custom backend site to Shopify. For example on a customer I would like a link - "View on custom dashboard [http://app.sample.com/admin/{customerid}]". We replicate Shopify's data so all ID's correlate - just need to change the URL.
So I created an app on my Partner account. I set up all the links, but I cannot figure out how to install this app onto my Store. The App insists I list the app publicly - I cannot see another way around this.
As a workaround I put together a little bookmark for the team as it's simply just changing the urls, but it's a real nice-to-have to have it directly on Shopify.