I wish I had a better answer, but I honestly just stumble around it. I typically start by trying to understand how they structured their files, then I'll start diving into the code. I wouldn't try to "understand" it completely. Just look over it until you feel comfortable enough to try to make some modifications.
Michael's code looks clean and well organized. Shouldn't be terribly difficult for someone proficient at JS.
Another thing I do is try and replicate one core feature of the thing I'm trying to understand. Like others have suggested, I like using debuggers. Recently, I wondered how debuggers work. So I built the following to find out.
Michael's code looks clean and well organized. Shouldn't be terribly difficult for someone proficient at JS.