When I read I like to take notes seperate from the document I am reading. Think of this as sitting at a desk reading a book while taking notes in a seperate notebook. I have tons of apps that will let me highlight and mark up the source material (PDF annotation) but cant find any that give me a dedicated notes area (with a split-screenish) design.
Some apps let you take notes on the sides of individual pages. This does not work for me because my notes often span more than one page or even one chapter. I might for example be making an outline that has points from various parts of a long document. Takng notes directly on a PDF forces me to be stuck to a single page.
If anyone else takes notes like this and has found a good solution or app please let me know. We can't have two apps up on an ipad screen like we can on a desktop computer but there is no reason why an app cant be a reader and notebook built into one screen.