If I understand the question, the typical workflow is to apply a Motion Builder Actor control rig to both the imported .bvh skeleton and your character's rig. Since the control rigs are hierarchically identical, you can easily retarget the data from the .bvh to the character. Then, you want to bake the motion down to the character's rig.
After that, you can tell the character's control rig to stop using the .bvh. This frees you up to use the control rig to edit the mocap motion beneath it. Naturally, if you edit the motion, you'll need to bake it down again before exporting the data for your intended use.
If you go over to
3D Buzz, and dig deep into their free tutorials archives, you'll find some very helpful introductory videos on setting up and using Motion Builder. The videos are several years old but the workflow really hasn't changed much. (3D Buzz is a pay site but I think their old tutorials are still free there.)
Hope this helps.
G.