My girls are constantly scratching out the bedding from the nest boxes.
A photo might help us see something, but this often means the lips on the nest are not high enough. You might try raising the lips a few inches.
They lay on the bare floor.
Are you using fake eggs in the nests to show them where to lay, I use golf balls. When mine were scratching the fake eggs out (before I raised the lip) mine would lay on the floor next to the golf ball. If you are not using fake eggs, you might try them. Put one on each nest. Sometimes they work.
They also only use one box.
That is pretty normal. By putting a golf ball in each nest I get mine to spread the laying out a bit but I still get half or more in one nest.
The other very weird thing I've discovered is two girls using the same nest box at the same time. Usually it's the two biggest girls in the flock.
Only two? I often have three in the nest laying at the same time. Haven't seen four yet. Again, very normal.
For the nesting material any suggestions on how to soften the floor?
What are you currently using for nest bedding? Some of the things different people on this forum use are straw, hay, wood shavings, carpet, dried leaves, Spanish moss, feed bags, shredded paper, sand, rags, and probably a few things I'm forgetting. I cut some tall grass from where I don't mow or weed eat and dry that so pretty close to hay.
Do you mean the coop floor or the run? Not exactly sure. In the coop some people use dirt, sand, wood chips, wood shavings, hay, straw, dried leaves, or some other things. Some people turn their coop or run floor into a compost pile so anything that goes into a compost pile.
The basic rule for a coop floor and the run as much as you can is to keep it pretty dry. Other than that there are no rules.