In How to Read a Book , Mortimer J. Adler and Charles Van Doren classified four levels of reading: Elementary Reading, Inspectional reading, Analytical reading, Syntopical reading.
Here is a blogpost summarizes it:
I think MarginNote and Highlights are suitable for the third level reading. With them, you can chew and digest papers or books, i.e. a more in-depth reading.
LiquidText for me is more suitable for the fourth level reading, whose focus is comparison. So you need a software to help you compare or contrast ideas & arguments of a specific subject matter from different papers/books. Based on this, you develop our own ideas and theories.