You are basically asking for a summary of the domain called Pattern Analysis: Something that I used to run a semester course on at the University of Canberra. Are there good textbooks on the subject? Unfortunately no. And yes, I should write one but have always found more productive avenues to invest time in (e.g., http://spatial.ala.org.au
The Help file with PATN is comprehensive and does have browse sequences that permit stepping through the functions in a logical manner. The best idea for getting a good idea on how to approach an analysis is probably the case studies on the PATN web site: http://www.patn.com.au/examples/default.htm
. There is a general case study using socio-economic data and another using a very nice biological dataset with associated environmental parameters for Antarctic benthic critters. If you work your way through these, I'd hope that you would get a good idea on the strategies and reasoning.
I'm open and then some to other chiming in here...