It seems that this message has fallen through the cracks and did not get answered. If you have not figured out the answer by now and still interested in how to do it then let us know.
In short: 1. This operation is called skull stripping and you can use SwissSkullStripper extensions for this. 2. You would need to specify how exactly you would like to fuse the images. For example, would you like to export a colored image where brightness of each voxel comes from the master volume and segments specify color hue?