Goodreader is the best free app I have found for editing, making notes and general research on the iPad. Through Dropbox or simple email, get the pdf onto your iPad. A pdf immediately becomes a book in the Goodreader program. So you can flip the pages just as if you were in the Kindle program.
The great news is that there is a vast menu for annotations for that pdf: text boxes, hand written notes, highlights. They are all available in a range of color to suit your creative fancy.
Once you finish your changes on the pdf, you can save them as a “flattened annotated file”. What does that mean? Essentially, all your notes are, of course, saved; but you also have a complete index of every textbox change that has been made.
The index is hyperlinked to the specific page change as well as from the index back to the specific change. It is a great resource. The index becomes a bible for your future work. It’s a terrific document for ticking off changes from one single document. Depending on the next stage of work, your index could be one page or a hundred pages. Somehow, the index makes the work seem less daunting.
This is a great tool for writers who want to get a “fresh” view of their work by looking at in another format. It’s a heck of a lot more efficient than Truman Capote’s method of sticking the manuscript in the desk drawer and pulling it out a month later. That works, too – but sometimes we do not have that luxury of time.
I am not a “Pages” fan for editing. As hard as Apple pushes, I do not think Pages will replace the WORD doc in the near future. Apparently, you can also edit straight onto the Goodreader program with a WORD doc but I have not tried it out. But for PDF on iPad, I don’t believe there is an easier, more impactful app out there.