Are they Mobi files? If you can see them in iTunes then they must be ePubs which aren't compatible with Kindle's or Kindle Apps, so they'd need converting to Mobi format. Are the books DRM'd, if so and they're ePubs the DRM would have to be removed to be able to convert.
If you have Mobi files here's some info on sideloading...
http://www.macworld.com/article/1157066/kindle_app.html
...or you can email them to the apps email address and they'll be downloadable in app.