This quarter I used iPad to work with digital copies of the assigned readings in my class. I used a combo of three applications, iAnnotate, NoteTaker and iA Writer to replicate exclusively on the iPad what I usually do differently.
I used two methods to load the readings, one directly from Coursework, through the Web download capability of iAnnotate, and via iTunes. iAnnotate needs some time to process the downloaded files, if they are large, but it is acceptable. The main glitch is that all downloaded files end up in one generic place, (depending on which upload methd you use it is in "Recents" or in "Web downloads"). I have a number of documents in iAnnotate, and all are organized in folders. It proved to be a real nuisance to have to find the files and move them into the folder I had created for the class readings. This could be easily remedied if iTunes recognized the iAnnotate folder structure, which it does not currently, and if Web download would allow to choose a download location.
Reading social science research papers is different from reading a novel. I find myself jumping back and forth a lot. What was the title of this section again? What was that model that the author used to run this regression? Sometimes, all figures are added at the end of the paper. Doing this in iAnnotate is a drag, as you are left with scrolling. I ended up adding bookmarks for each section, but it requires some marking up of your document simply in preparation to work with it. I also used the capability to jump to a certain page number, which of course requires you to know about which page number you want to go to.
Annotations is what iAnnotate is made for and they work reasonably well. I did fight with the interface at times, misinterpreting the "x" (for close annotation tool) as "x" for delete, for example. I worked with a stylus to mainly underline sections and I very occasionally used the free-hand drawing tool, which is not very precise. I additionally used iA Writer to type out more extensive comments, questions and summaries, which requires to add page numbers to refer back to iAnnotate, then switch between the two apps and find that page.
During class discussions I used NoteTaker to quickly take down additional comments, questions, or remarks. I am unable to type fast enough, and NoteTaker affords me the flexibility to include sketches or graphs, which I do quite frequently. Again, there is no way to directly link these notes to the article. The iPad's multitasking capability has made it very easy to switch between apps, wich was very useful for my needs here. But what if applications like these could really talk to each other, and we could conceive of a modular toolbox?
 For how to get articles in Coursework see my experience with JotNot, a tool I have come to really appreciate.