That reference manual is hidden behind a mystery-meat icon, is difficult to navigate, can't really be searched, and (last time I looked) was out of date. I found it nothing but frustrating when I was trying to get started. The one thing that saved me from abandoning my project altogether was this:
draft Vassal Module Designer's Guide:
http://www.mediafire.com/?0tabexd3typmma7Download this excellent word doc to your hard drive and don't waste your time on that little green icon. Just be aware that it's a work in progress and you will still need to come on the forums and beg people to explain things to you.
I would like to credit and thank the author, but I can't find a name anywhere. (In fact, I was barely able to find my way back to the link to the file; this document seems like one of Vassal's best-kept secrets!)