I enjoy reading the books that I have downloaded into ibooks - but many of the books I want are not available in their store - but are at Amazon. If I use the Kindle app, do the downloaded books go into the ibooks library or is a Kindle library started separately - and is the formatting kindle-like or ibooks-like - I much prefer the latter.

The books go to the kindle library and your progress is synced across all your devices using the kindle app. I prefer this because I can read while I'm waiting for things using my blackberry, then open my laptop and read on my break at work, then come home and read on iPad....simple and efficient. I would like more control over formatting but I like it better than the two page book thing in iBooks. Takes up too much space!