Just as you should write your own paper in smaller sections, you should consider reading academic articles in sections.
Some articles (like my example here) are lengthy (28 pages, in this case), which makes understanding, absorbing, and annotating a piece difficult. We can lose steam the further we get into a long article, book chapter, or book.
The solution? Eat that elephant one bite at a time!
Go section by section on your first read-through. Pay attention to the spots that confuse you (annotation, anyone?) to come back to later, whether this be on a second read-through or later in your first when things start to click.