I think it is important to include only the books that you are committed to finishing in the scope since the charts are based on how many books/verses you are trying to finish by a certain date. So if you are in a NT project but the church asks for 2-3 key Psalms, I would not put the entire book of Psalms in my scope or my progress charts would never show me as finished.
A less obvious factor in getting the most out of the progress charts is setting a target completion date in the Paratext Registry. If you are able to log in to the registry site directly you will see that a completion date field is there that was not available when you first registered your project. It can be easier to initiate this in Paratext by going to the project properties window in you project and clicking on the manage registration link.