No problem Ponyboy.

First up, I should say that I havn't covered animation in Maya too much. If you post up your troubles with these rigging and animation chapters in the animation part of the forum, there will be folks there who can help. Perhaps even a search for 'joint orientation', as I'm sure similar questions have been asked in the past.

With that said...joint orientation, the several times that Ive come across it, I find awkward too. To change the orientation of the joints, go into component mode...(see screenshot). When in component mode, click the question mark filter (number 2) and you should see the local axes of the joints. You can then use the rotate tool to manually change the orientation. In the 'Skeleton' menu of the animation menuset theres a reorient joint tool also...if you click the dialogue box option on the end, you can select your settings, and then reorient the joint that way too.

Hope that helps a little...