I don't think you're going to find a one-magic-tool solution to what you're looking for. The information you're trying to manage is too different.
I would solve the problem something like this, given my personal productivity systems:
- When the reading assignment is made, add an entry to my Projects list (Evernote). Attach the document to the note, or if the document is in a format that can't be attached include a link to where the document can be found. Tag the entry with a due date (e.g. _due20130115). Also tag the entry with a project identifier, e.g. p-econ503-friedman01
- Add an entry to my @Reading task list (RememberTheMilk) - Read next section in p-econ503-friedman01
- Possibly block time on my Google calendar to do the reading. Especially if you need to be done by a certain date, getting it on the calendar is a big help. If I were being super effective, I might include a link to the Evernote Project entry in the calendar entry notes.
- While doing the reading, make notes either in the Projects list, or in additional notes in Evernote linked by the p-econ503-friedman01 project identifier tag. Which I would do depends on how long the reading is and how extensive the notes need to be. For a journal article, I'd probably make notes in the Project entry, for a book I'd think seriously about separating notes by chapter or major theme.
Given the number of platforms Evernote supports and offline notebooks (for "pro" accounts) you should have access to your material most of the time.
I've been pretty successful at keeping up with professional reading in little bits of time like standing in line at the grocery store using this kind of approach.