At this point in the process, you have committed to a topic, found resources on it, and now are trying to glean information from those sources. The page linked above provides some note taking tips, ways to avoid plagiarism, and 5 different note taking styles (also described below). Pick the style that works best for you.
The Cornell Method uses a two-column approach to note taking.
Cornell Notes - wikipedia http://en.wikipedia.org/wiki/Cornell_Notes
The Outline Method is a very structed way of note-taking.
The Mapping Method is a very visual way of organizing your notes and information.
The Charting Method utilizes a chart-structure as a way of organizing your notes.
The Sentence Method is the most basic notes-taking method.