Use a pen and paper, or images/graphs/charts in general, to figure out which parts belong where and draw some arrows and so on.
This helps you build and see the image that will then be refined in your mind as you become more comfortable with it.
I used a similar approach attacking a hellish system that had 10 singletons all #including each other. I had to redraw it a few times in order to fit everything, but seeing it in front of you helps.
It might also be useful to use Graphviz when constructing dependency graphs. That way you only have to list everything (in a text file) and then the tool will draw the (often unsightly) picture. (This is what I did for the #include dependencies in above syste,)