When you plot your animation either on the take or on the skeleton/control rig it takes any key you’ve made and turns it into the new ‘original’ data (which is a key on everyframe). As far as I know there’s no way of splitting these up.
You might want to try adjusting the fcurves before making any changes and adding keys with the IK/effectors. But if you prefer to work the other way around, you’ll be adjusting the orginial data and most likely your new effector keys will be affected by those changes since they’re a layer ontop of the original data, and you’ll be having to reset the effector’s keys to the way you wanted them BEFORE you made changes to the fcurves. (I hope I didn’t jumble that up too much, haha)
Choosing a workflow is much different for MotionBuilder than if you’re using Maya, Max or any other software to animate in. It might take a few files before you find a workflow that fits your wants/needs.