A lot of people have found that painting the Flow frames with melted wax, or even rubbing some burr comb on them will encourage the bees to use them. It also signals that this is part of the hive, as the wax makes it smell of home to them - might discourage the swarming.
I wouldn’t move the frames around - it will likely mess up all the bee space in the box. If you really need to thin out the bees, you could do a split - even a small split into a nucleus box might help remove the swarming urge.