I've used the Scene function for this before, although there is no manipulate (which I also preferred) I found that I can get near the same functionality by dropping the compass onto the component I want to move, and dragging along the compass axes to move in a particular direction / rotate about a specific axis.
Alternatively if the rotations/translations are defined as constraints, and you wanted to 'manipulate with respect to constraints', you could create a scene (with the limited override function, I forgot exactly what it's called) when the master assembly is at one state, exit the scene, move the assembly to desired position no. 2 and create a new scene at that new position (again with limited override functionality). The positions of the components should reflect where they were when the scene was created. I haven't tried this in about a year, though, so don't shoot me if I remembered incorrectly...