How do you keep track of large projects?

Question

When dealing with a project that has many different files, I always seem to loose track of how the parts interact with one another. I've never really had much of a problem understanding smaller components in isolation, but as the complexity of the project increases, I find myself unable to mentally construct an understanding of what is going on. I notice this especially with OOP projects, as the number of methods and source files increase.

My background: I'm a self-taught web programmer. I've dealt mostly with python for quick and dirty scripts, but I've also done a few basic django projects. I like web frameworks such as flask, because in the simplicity of a single-file layout, I can easily keep track (mostly) of what is going on.

I now find myself in a situation where I need to interact with a large Zend Framework PHP project that someone else developed, and I'm overwhelmed with trying to understand the code spread out to numerous files.

What techniques and processes have you found useful to understand a large code base that someone else has developed? Is there any particular diagram that you find helps you grasp the larger picture?