I rarely use KOReader so keep in mind that I might be wrong with my conclusions but as far as I could tell KOReader doesn't offer an option to "flatten" all subfolders inside the folder that was set as Home folder in KOReader and to then display just a list of all books. So the only workaround to get just list of books without any folders is to not put books in subfolders
just dump them all at root level of Home folder. If you're using the built-in support for connecting to Calibre as a wireless device then you'll need to adjust save template for that device in order to control how the filename and folder structure will look like once the books are transferred to KOReader.
Also a huge bummer with KOReader is that as far as I could tell is that when listing books it doesn't offer ability to sort by author or title metadata! It can sort only based on filenames, file sizes, date added, date last opened.
So to workaround those unfortunate limitations I had to make Calibre construct filename as "author - series - series index - title" so that when books / files are sorted by filename they are order by author and books that are part of a series are ordered in correct order.
But then there is no way to sort by book titles...
For cover thumbnails in KOReader you need to switch it to what it calls "mosaic".