Have a look at the iAnnotate app. You can easily insert images into (onto?) a PDF, in addition to be able to make text or handwritten annotations. Then, when you are done, you can flatten the image so your changes are permanently in the image.
it's also got a Dropbox upload capability so it's easier to download/upload files. This makes it easier to transfer stuff versus e-mail or hooking the iPad up to iTunes.
Just a thought...
Marilyn