Please have patience with me

... I am new to the eReader world and love that I can download books directly onto my new Kobo WiFi. However, after some conversation with a KOBO tech during my initial setup, I thought I remembered him telling me that I could not download from Amazon or Barnes and Noble. Is this true? Also, I've downloaded a book or two through the Kobo Bookstore..how do I "manage" my books through Calibre?