The short version is you have to ask the right questions. Naturally for every theorem or equation, there are 3 big questions:
1) What does the theorem/equation say? What's the intuition behind it?
2) Why is it true?
3) How does one come up with it?
One must ask these questions in the exact order. To understand what the equation really means, you should break it down further to smaller components. What is this variable? What does it represent? What is the intuition behind what it represents? What's the implication when the variable increases, decreases, etc? Do that for every single component in the equation/theorem. One should fully understand the intuition and clearly describe all quantities before trying to look at the equation/theorem as a whole.
To understand why an equation/theorem is true you need to build up a repertoire of theorems related to the quantities of interest. The bigger your repertoire, the easier you can prove or disprove something. The more advanced way is to build up intuition around the quantities of interest then come up with intuitive hypotheses. The hypotheses are often easier to prove/disprove. The process repeats.