This might be a question that is easy to answer... I am trying to rotate an Object along the length of it in a 3D-Space, however the manipulator is arranged in a way, where it would need two axis to rotate it in that way. Is there any way to rearrange the manipulator without influencing the Object?
If you really mean a 3D object as in "polygonal mesh via Cineware/ C4D Lite or Element 3D" then this will have to be handled by fixing this in the 3D program by opening up the models and adjusting their pivot points and scene orientation. For AE layers there is no way to adjust the orientation of the anchor point, only its position. Therefore your setup may simply require soem parenting tricks or similar, but it's really impossible to understand your issue without a better explanation and a screenshot at least.