If the supers you installed above the queen excluder had just foundation in them, then I am not surprised the bees ignored them. If you are going to use an excluder, you need something above it to lure the bees thru it. A frame or two of uncapped brood works nicely. If you only have one brood chamber, then it is very likely the queen has moved up and is laying in the supers. If you want to run with the excluder, move the queen back down to the bottom and re-install the excluder. The brood she had laid in the supers will keep the bees above the excluder. Once it hatches, the bees will continue to work above the excluder and you won't have any more brood up there.
If your only running one brood chamber, you have to keep an eye on it more so that the queen doesn't get honey bound and run out of places to lay. If you are located 5 hours away and don't get there that often, I would highly suggest having a bigger brood area.