Lots of complex matters implied in your questions, but trying to simplify...
There are two concepts that can be dealt with separately: physical file location(s), and how the files are listed, grouped, sorted, etc, in Media Center's database (aka library).
MC doesn't really care where you store music files, or what their subfolders might be. The database views of music files (individual tracks) are presented to you based on tag data and view design and config.
MC has a configurable expression/formula for how folders and tracks are named, therefore how the physical files are organized. It is typically applied when you rip new files. But if you are looking at an existing set of folders/files, accessing them via MC, it won't change that arrangement (though it can, using the Rename, Move, Copy Files tool). MC of course knows where the files are, but this doesn't matter as you look at tracks in the database.
To make the database sort tracks the same way you've organized them in folders, you need to give the database sufficient information, AND set the view to use it to sort. Note that you can organize the database view this way even if the tracks are NOT grouped a certain way in folder (by album and CD, for instance) -- every file could be in a random location and it wouldn't matter to how you tag and view the tracks.
For multi-CD sets, I use the Disc # and Track # fields. Then I click the Track and Disc columns (in that order, so Track is a sort subset of Disc) to tell MC to first sort by Disc #, then by Track #. That will provide what you want. (If you don't see these columns in the view you are using, right-click the column header row and select these fields. You can then drag the columns to where you want them.)
In a view that has multiple albums, some with multiple discs, I sort by Track, Disc, Album (in that order).
If what you want in a view is notably different from the stock views, or you don't want to alter a stock view, you can create a new view. Set it up just as you like. Then (for safety), Save the view. My database has several custom views for this purpose, because I use a bunch of custom fields so created views to better work with them.
If you decide to modify any stock views, also save the modified view so it can be reapplied if (when) MC reverts the stock views to their stock design. I do this for certain stock playlists that MC controls, notably Recently Ripped and Recently Imported, where I want to see and work with different columns.
(Actually, I like 90% of my views to be identical other than grouping/sorting, so I can jump around within the database and always see the same data organization. But note that due to an MC design quirk, visually-identical saved custom view design and custom playlist design can't be interchanged -- unless you dive in and hack the files, as described elsewhere.)
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Topic: M2Tech Hiface problem [solved] (Read 5059 times)