You can use any prewriting method that works for you. Last semester, one student’s maps looked just like diagrammed sentences, which was very cool. Another, who was brilliant and who had a mind like a file cabinet (very admirable!) preferred to create old-fashioned outlines, complete with roman numerals, etc. As for me, my mind works differently, so I typically use what’s called “mind mapping.”
You can–and will–do lots of prewriting/mapping with pencil and paper, but you might want to experiment with software too. A great open-source program is FreeMind. Or you can just draw text boxes in word processing programs. For Mac users, try MindNode, available in both free and pro versions.
(Top image source courtesy of Wikimedia Commons; bottom image from old web page of Govt. of S. Australia)