The important part of that is that calibre is not matching some books on the device to books in the library. The rest is either because of that, or doesn't matter (the directory structure is completely irrelevant).
The usual reason that books on the Kobo device do not match with those in calibre is that the books have multiple authors. Unfortunately, the Kobo device does not read the authors in the way that calibre normally writes them. This is a lack on Kobo's side, but, is probably within the specifications. It means that for sideloaded books, the device will usually only have one author. For this reason I recommend using a metadata plugboard to set the authors how the device will best handle them. This is to set the authors using the template:
Code:
program: raw_list('authors', ', ')
With this, books with multiple authors are much more likely to be matched after being sent to the device.
There are other reasons for books not matching. The publishers are to blame for putting extra rubbish in the title (usually the series info or some sort of subtitle) which means the title doesn't match the one in calibre. That is mainly an issue with books downloaded directly to the device or otherwise not put on the device by calibre.
To fix this for books already on the device, you need to manually match them. When you have the device connected, device list and right-click on a book that is not matched. Select the option "Match book to library". In the dialog that comes up, search for the book and select it then press the OK button. Once you have matched the books, right-click on the device button and select "Update cached metadata on device". This updates a file on the device that calibre uses to assist it in matching the books when accessing the device. After this is done, the books should match automatically whenever the device is connected.
And if the books are matched, then the collection management should be done for the books (assuming it is configured correctly).