You can copy your ebooks into any directory that does not start with a dot. Copying them into a directory called books will work, copying them into .kobo will not work. Once remove the Kobo from your computer, it will find the new books and spend a few minutes collecting information about those book (e.g. title, author, cover) so that it can add them to its library. When that it done, you can access them just like any book purchased from Kobo.