Candi,
Remember you probably got 10,000+ bees in your package. You have a one in 10,000 chance of mashing the queen, so don't worry about it. And the odds only get greater as the population in the hive increases. Yes, you might crush her, but if she has already laid eggs the girls will just make a new queen from the eggs she left behind. So don't sweat it.
Leave them alone for a while and let the bees be bees. They know how to take care of themselves. Open them back up in a couple of weeks and you most likely will see capped brood, larva, eggs....and maybe even a queen.
A TIP: I always carry a queen clip and a marking pen in my bee jacket so if I do spot a queen, I can mark her right then and make her easier to spot in the future.