Bees not building where they are supposed to
OK. So I'm a total noob and this is my first hive. Please don't beat me up too much, but I need help. I captured a swarm by a dumpster and let them live in a cardboard box with a hole in it for entry/ exit while feeding them raw honey for a week while my hive was in the mail. I managed to get them into the hive after a week of living in the box with little issue. (They were NOT happy) I put all of the comb they made in the bottom of the hive so they could still have the larvae in the comb. It seemed like a good idea at the time. There was a lot more comb in the cardboard box than I imagined would be in there.
The bees just keep adding to the comb at the bottom of the hive instead of building on the bars. My boyfriend has the idea that we should let them stalagmite the comb up to the bars, then cut off the bottom part. I think that will take too long, but I don't have any better idea about how to get them to build from the top bars. My hive has a window so I keep glaring at them from time to time but that doesn't help either.
Any suggestions on what to do now? As a bug person, I really don't want to kill any larvae if I don't have to.