I have been going over My System for the past few weeks as part of the study strategy portion of my study schedule. I think the best way to go over the content of the book is to go over The Elements section going over each example carefully. Luckily I have a Chessbase file with all of the diagrams setup which saves me a lot of time. I am annotating the diagrams while reading the book notes. Once I go over The Elements section, I plan on going over it a second time before I begin on Part 2: Positional Play. This will ensure that I have a good understanding of the foundations of Nimzowitsch’s System before I get into the more advanced content. I am also going over the illustrative games whenever Nimzowitsch calls for it.
In addition, it is helpful to have a copy of Chess Praxis, which has additional illustrative games, as well as a more condensed and modern explanation of key concepts.