Hello @mikemo and welcome to the forum.
I do not fully understand what you are trying to achieve but I’ll try to answer the best way that I can.
When building a rig with mGear most of the components will create joints for you to use later on. Those joints have their transform values (translate, rotate, scale, shear attributes) connected to the rig system using matrix calculations and the attributes on the joint are set to non keyable.
If you are trying to use the joints that mGear create those are already connected to the rig. This means that if you want to override how the joint is been driven by the rig you need to first break the connections to the nodes been use to drive the joint (check in the node editor)… Or you can simple replace some of the drivers connections to the nodes that drives the joint.
I hope this helps you.
PS: Don’t know if this might be of any use for you but @Miquel did a video some time ago on how to hook an mGear rig to a mocap skeleton.