a real help for me understanding joint orientations was jason schleifer. also Jay told me quite a bit about it when I tried was trying to understand once. maybe you find something in an old thread of mine here
most important thing is to understand which axis you set for the joint pointing down on it. play a lot with local rotation axis. maybe construct a very basic joint chain and experiment a lot. understanding joint orientation comes with practice - believe me! create joints and orient. click each button in the menu a hundred times. this is a good intuitive approach learning about orienting joints.
Jason Schleifer´s site -> www.jonhandhisdog.com
also tutorials from Alex Alvarez were very informative!
if you have a specific question later on, just ask.
everything starts and ends in the right place at the right time.