Having trouble with backing up my iBooks and possibly a corrupted file

I have several iPad ebook and PDF purchases that were not from the iTunes store that I would like to backup somewhere, either in the cloud or on my Mac. I cannot figure out how to do this. When I tried syncing books in iTunes, it wants to replace everything on the iPad with what's on my Mac, which would be a disaster. If anything happens to my iPad, I will lose these books. How can I back them up?

In a related question, the issue that started all this was an epub I purchased from LexisNexis, a rather large book (8 mb, thousands of pages). The first time I opened it, it was fine, but after the second time I think the file got corrupted because it freezes whenever I try to navigate anywhere in the book. If the file has gotten corrupted, I have no idea how to delete the book so that I can reinstall it. I have no idea what to do. I know this is technically two questions in one post (sorry) but I'm really at a loss. I need that book, and I'd really like the peace of mind knowing my books are backed up somewhere if my iPad dies. Thanks!

Curlygc