Clickbank ebooks are pdf books; one example is Lisa's Niche Website Success. You can use any pdf program or convert to pdf from Word, etc. It is the easiest way to go.
Since the cover is in the pdf you can design or have someone design it as you want. It is essentially just another page in the book although you will need something more for publishing on your site as advertisement.
Kindle has their own formatting which is more complicated obviously as you can see a lot of publishers have pages that haven't turned out too well when viewed at different sizes, etc., especially things like the table of contents.
Clickbank books get higher refund rates but you make more profit for sales to start with. There are pros and cons each way.