Hi Wesley, rigging is a challenge sometimes and I totally agree with you about these issues that crop up. From what you mention, it sounds like you need to check your joint orientations first and test them out constantly before even attempting to make them functional.
You could look up tutorials or explanations on joint orientations online or check Maya help for more information on that. Here's a link to start you off:
http://forums.cgsociety.org/archive/index.php/t-184674.html
I hope I have helped and not strayed away from what you were expecting.
Thanks,
Sam