With regards to control objects, I find its best to create said object and move and postition it to the joint in question, then use v to snap the control to the joint,then freeze its transforms. select the control, then shift select the joint, go to the constrain menu>point, then select the joint then shift select the control, and go again to constrain and orient. that should keep every thing in alignment.

There are a few scripts out there that can do it better, I have one I'll dig out and post up. It allows joint rotations to be zero (yes the joint not a control) wherever you place them or rotate them so you dont have issues with having to put controls in place, you can hit the joint and it will zero out evn at an acute angle...clever shit if I do say so.

I'll have a look for it

Jay