Ashtok,
I would start at the top level. This diagram should be somewhat simple and just invoke a number of subVIs. Once this top level VI is understood, I would start with one subVI (recursively, of course) to understand, then move to another. At each level, add comments so that no one has to struggle like this again. Chances are that you are not understanding this code because it was not commented. This happens because some say adding comments in a graphical language is very difficult. However, it is easy if you document ideas and concepts (you could always document every single thing, but that is what the VI Properties, documentation is for as well).
Randy Hoskin
Applications Engineer
National Instruments
http://www.ni.com/ask