Hello Bill, I think you added the super too early when your saying you found 2 frames not built out so they were not put to use. The brood box is needing to be packed out with bees, all the frames in it in use for brood and stores before adding a super. A bee colony will concentrate its efforts as close as possible to the brood area.
I would check out with other bee keepers in your area as to the use of a single, a single and a medium or a double brood set up for your climate, that will depend of the temperature and length of your Winter.
I didn’t find spraying Flow Frames a success in having the bees work in the super other than to take up the sugar water and move it down into the brood. I experimented with my new Flow Frames and found that brushing on melted wax was a help supply them with wax to seal the gaps in the frames quicker.
If the bees are not working in the super it is that they don’t need the super, either the colony isn’t big enough or they don’t need the room for stores.