How can I include a detailed protocol describing the diagrams of an in-class biology experiment?

A "detailed protocol" is really just a fancy way of saying "the instructions". We just use this vocabulary to indicate the subtle but importance between following instructions like you would follow a recipe, and following a series of rules, regulations and guidelines that are a little more flexible and adaptive to your particular situation.
To incorporate diagrams into a protocol, you need to understand and prioritize the purpose of the experiment and the way in which the diagrams will meet or lead toward that purpose. Generally speaking, diagrams will either be a part of the procedure that have already been provided to you, to facilitate their execution, or they'll be something you have to create in order to describe your observations and results. If there are multiple diagrams, it helps to give them separate names and numbers, such as "Figure 1", and refer to them in this manner consistently throughout the procedure.
If a diagram is too complicated to refer to as a single figure, it can either be broken up into smaller diagrams, or given sub-labels within the diagram itself. A good example of this is found in many model kit diagrams. You can also refer to specific physical locations in the diagram with simple language, such as "the top left quarter of the diagram" - this is totally normal and acceptable even in college-level science.
If the protocol has not been provided to you already, review the materials given to you for the experiment, or the notes you took, and rewrite everything in sequential order, with specific attention to safety procedures and including all relevant information when it's called for. For example, many students will write a procedure without taking explanations into account, such as saying "on the diagram" without specifying which one. Make sure that all references are specific enough that a person who wasn't present for the experiment would be able to do it with little or no guidance.