It may well have worked the way you said because there have been all sorts of issues with the Core not recognising shares. I think the latest firmware is supposed to have fixed that....
But the theory is that you have one music store, which can be but doesn't have to be the internal disc - if you have installed one, and multiple shares. The store is where the Core saves its own rips. You can save downloaded files or rips made on a PC in the downloads folder of the store by moving or copying them with a PC. You can also save downloads or rips made on a PC on any disc which is a share.
A disc is a share if you define it as such in the app. You can have multiple shares. I believe you are only supposed to have one store, but from early discussions on the forum the Core seems a bit more agnostic than that and you can apparently define more than one store. Exactly what happens if you do is unclear to me!
Howrver many stores and shares you have, they should automatically index and you can then select and play them from the app. For a while I had a Unitiserve on my network as well as a Core and if I defined the Unitiserve as a share, I could select the music on that in the app alongside the same music in the Core.
You can also import music into the Core. If you use the import function in the app, it should offer you all of the shares and you can select one of them. The files are then copied into the music store. If the rip was made on a Naim server, the import puts it into the Music/MQ folder in the Core's music store and if it wasn't made on a Naim server, the import puts it into the downloads folder.
Some of what I have read suggests that if there is anothet Naim server on the network, the Core will offer it as an import source without you defining it as a share, but that never worked for me. I had to define the US as a share, import the music and then I delete it as a share.
Anyway as long as it works for you, you might want to just let it go at that. One thing to avoid though is inadvertently importing so much into your music store that it becomes virtually full because (again from what has been discussed on the forum previously) the Core does not behave well in that situation and becomes extremely unpredictable in many of its operations, such that you might have to pull the music store, reformat it and start again.