One useful method we can employ almost immediately when encountering a new code base is to populate a mind map or flowchart that highlights not only the things we know but the things we aren't yet sure about. Here's a simplified example of such a diagram for a piece of medical software I once worked on:
As you can see, I have tried to outline my current understanding of the user flow and have also added questions or areas of confusion I am personally experiencing in the cloud annotations. Over time, as my understanding grows, I can add to this flowchart.
People learn in a huge variety of ways. This visual aid may be more useful for some people but less for others. There are also countless ways of composing such flowcharts. For the goal of personal understanding, it is best to use whatever works for you.