You're probably talking about the ailerons or landing gear of an imported model?

The easiest way is to open the moving part in the vertex modeling room and rotate it so that the hinge is aligned to the X axis. This probably means that you'll have to rotate the object back in the Assembly Room so that it's in correct position to the model. 

However, now that you've done these steps, if you select either Rotate or Universal Manipulator, you'll see that they now align with the X axis of the part in the Vertex Room. You can now use these tools to visually adjust to your hearts content!

Mark