You need to give them all the space they need. If they use it, fine. If they do not, then you just remove it later on. They may just put a little honey up there. I had the same experience before and if they do not fill it out, then you have several options.
1. You can take the frames they filled with honey and lower them into the bottom supers before winter.
2. You can take the frames with honey and freeze them to have on hand to give back to them if you need to feed them later on.
3. You can extract the honey if it is extra and they have capped it.
4. You can place the super over an inner cover and let them rob out the frames and clean up the frames.
Am I forgetting anything guys and gals???
Hope this helped
Annette