Sounds as if your colony is starting off well and growing normally. Don't worry about the queen going up. If there is a flow on, you could probably take out the feeder without any problems and it would open up the first box a bit but in my experience with all mediums, the queen will move up and down in the lower three - four boxes, sometimes even up into the fifth box if you don't use an excluder, but you can always move those frames. Again, all is well and sounds like your hive is thriving.