Getting a migraine here with all the productivity apps ... still don't know which ones are 'the best'.
I've tried two great apps called Readdle and iAnnotate. Excellent at marking up and annotating pdf docs (haven't tried annotating iWork or Office docs yet; hopefully the same). Huge is you can transfer them back and forth between iPad and laptop, and don't lose your markups when you open the file in Preview or App.
One thing though, is there a way to still see the 'rectangle or oval' annotations (from Preview) in the iPad apps? Impossible here. But when you transfer back the doc to your laptop, those are still on the pdf doc.
Thks for your help.