I thought I'd update on my new process of incorporating my iPad into as much of my routine as possible.
So far it's really worked out well. For my strategic management and required philosophy courses I read and annotate PDFs with PDF Expert 5. For my business law and Audit class use my logitech ultrathin keyboard with a combination of Word and Write. I also use Noteshelf and a cheap stylus for taking handwritten notes and figures. I decided to spend a lot of time looking into good apps that worked for my workflow.
So far it's been good aside from some slow/lag frustration with my iPad 3. I was having some Dropbox sync issues with PDF Expert, but reinstalling the app fixed that so far.
I also decided to try typing with the on screen keyboard during my (slow-ish) philosophy class. I'm not as fast or as accurate as with my logitech, but I was pleasantly surprised by how well and fast I can type with the iOS keyboard.
