I can sympathize with your predicament it's very confusing to a newcomer but we'll take it one step at a time.
Try moving any books in the Kepub folder to the main root directory or create a new folder named "books" or something and put them there.
A very rough guide to adding books to your Kobo eReader can be found here...
Click to open link
Quote:
Adding books (EPUB files) or PDFs to your Kobo eReader using your PC
You can connect your Kobo eReader to your Windows computer, and then drag and drop books into your eReader Library.
Connect your eReader to your computer using a Micro USB cable.
Tap Connect on your eReader.
When Windows prompts you, click Open folder to view files.
A desktop explorer window will open, showing the contents of your eReader.
Open a second desktop explorer window, and display the books you want to add to your eReader.
Drag and drop your books into the eReader.
Eject your eReader when you're finished.
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Once books are transferred and the eReader is ejected using windows "Safely Remove Hardware and Eject Media"
Remove the USB lead and the eReader should start to process the new content added, it looks for new files with the appropriate file extension and adds them to the device's database.
Then when you go to the menu button on the top left hand side of the screen and select "My Books" from the drop down menu you should see your eBooks displayed in your library.
You'll see it says "Books" just below that you should see it displays "Show:All" if it doesn't then touch "Show:" and a drop down menu should appear where you can select "Show:All"
Good luck, let me know how you get on.