My suggestion is to try to read proactively. If you're getting bogged down and taking overly copious notes, that tells me that you're reading passively: taking each passage as it arrives on the page, trying to hold it in mind, and hoping that enough accumulation will make the meaning of the work as a whole clear. That rarely works (I'm tempted to say 'never' with more advanced work). The human mind can retain vast amounts of knowledge, but knowledge and understanding are often at odds. One could memorize thousands of trees without really getting a sense for the forest, if you follow me...
A better approach (at least, it works for me) is to try to anticipate the argument. As you're reading, ask yourself: What is this passage leading to? Why is s'he including this point? Is it defending against a different position, advancing a chain of reasoning, exemplifying something said earlier? What does this passage lay the groundwork for? And then as you continue to read, see if you were right or wrong, and if you're wrong take the time to skim backwards to see what clues you missed. This allows you to enter into a kind of dialog with the author, one in which you can wrestle with the ideas as they are being presented rather than waiting for eventual revelation.
This ought to give you a clearer insight into what is central and what peripheral. You'll start to recognize hierarchical structures of logic (think of the sentence-paragraph-section-chapter hierarchy of a work, though not every work is laid out that way).
As a corollary, I'd suggest not marking a passage or adding a marginal note until you've gotten a paragraph or two beyond it. Only mark the text in four cases:
- When a passage is central to advancing the argument
- When an example is particularly informative or useful
- When the argument went in some direction you did not expect (a blindspot in your thinking you need to examine)
- When a passage grabs you and/or suggests a different line of reasoning you might want to explore later.
That should keep your markup sparse and on point for later review.