They are not big/strong enough to need more than 1 medium at this point, give them time to grow and they will use it. Depending on your climate (need to update your profile so we know where you are) swapping the boxes may be OK.
By instinct bees work downward. Think about a feral colony in a tree. Beekeepers prefer bees work up as it makes it easier on us to add more supers. Don't confuse our preference with theirs and assume there is an issue.
Best of Luck with your new hive.