I have a few books on Books on Board that are unread and when I got my Kobo Arc I just went to the website, downloaded some software I needed first and then downloaded the books. The only one I had a problem with was one that is no longer available in the UK, so I'll have to go back to reading that on my Sony.
I also have loads on E.books com site, and again they've downloaded fine to my Arc. I think what happens is they don't always download into the Kobo application but to another similar to Kindle books.
I've had it a week now and the only problem I have is with size. I expected with 7inch I would get 7 inch of text. Looks like I will be trading up to windows 8 after Christmas.