Hi Nicole,
Great question. Optimizing question timing is one of the hardest thing to figure out when writing the MCAT.
Typically, I will MAP a mechanism, reaction, or structure in a passage. In other words, I will note that the feature EXISTS in the passage, BRIEFLY look at it and noting its general features before moving on to the rest of the passage.
For example, mechanisms or reactions, I'll see if I can quickly recognize any steps (acid-base reactions, solvents, reagents, products, functional groups). Otherwise, I simply note that there IS a mechanism or reaction in the passage. You will find that questions typically refer to only one or two steps of a mechanism. Understanding the mechanism in great detail is NOT NECESSARY.
For structures, I note the existence of the structure (i.e. there's a molecule there), and see if I can quickly spot any important functional groups. Otherwise, I move on and continue with the rest of the passage.
The nature of the questions will then let me know if I need to look back at the passage and these mapped locations or not.
Try this technique with some passage-based questions and let me know if that helps. 😄