Hello Gavriel. Can you explain and give more context to your problem? Also post some screenshots that illustrate things a little bit more. As far as I can remember, bones Y axis are like the Z axis for normal objects I believe. I think for bones Y is up, but I’m not sure, the other guys will know more. In the mean time, have you watched the rigging fundamentals:
https://cgcookie.com/courses/core-fundamentals-of-rigging-blender
