I think people really overemphasize the strategy of "mapping". When I was in the TPR course last year and even right now in the Kaplan course, mapping is a strategy taught as if its the blood and bones of the VR. I disagree with it vehemently.
Making some kind of notes, outlines, etc. on paper during your VR is not only mental distraction but also wasteful for your time.
What you should be doing is mental mapping!!! In order to practice this, you need to get good at general reading comprehension, and this is where I think NYT, Economist, etc. come in real handy because you can go to the Op-Ed pieces and read casually and try to create a mental outline/map of the passage arguments and assertions. Every claim in passage is stated for a reason and the author may immediately support it or support it at the very end. You have to understand relationships between presented ideas and reading comprehension is something you can do to really improve on that.
It might actually take you practice physically making maps on the paper but for the actual MCAT exam, mental mapping is the way to go, physical mapping not so.