I have not downloaded books from Amazon to the iPad, and I use a Mac and iTunes, so my method may be different. I use Bluefire Reader, Overdrive, and iBooks. Bluefire uses Adobe Digital Editions on the Mac to translate books downloaded from the library, then I upload them with iTunes. With Overdrive and iBooks I can download directly from the iPad. However, I use iTunes to manage all of them. When I do my sync, under the apps tab, there is a section to click on the various types of reader programs. From there, I click on books to delete or add.
Have you tried doing a google search for something like "delete amazon downloaded books from iPad" ? Google searches have been my go to source for learning how to do things like this.
