I am a bit lost with all this at the moment but found a learning edition of a piece of software that may help me called endorphin. I think I simply import my characters skeleton and then fit it to the software's base skeleton. I can then run my fbx files and create my animation in there and once finished export my skeleton out with the animation back into maya.
I cannot really understand how to use mb at the moment and may come back to it when I am not in a rush to get things done. For now I just need something quick and easy so I can knock out the animation for some characters in a few days.

Cheers for your help guys, a lot of it is going over my head since I am new with animating characters but I am sure I will get there in the end. Damm life was a lot easier animating in 2d just a lot more time consuming.