I got my girls 3 months ago, and to begin with all 3 of them tried to sleep in two nesting boxes - a bit of a squeeze! Following advice from others on BYC I spent every night picking them up and putting them on the perches, and blocking the nesting boxes off with a bit of cardboard in front of them. It seemed to take forever, but in reality it must only have been about 3 weeks until the girls got the message and stopped going into the boxes at night.
I did make one major change in that time - the perches that came with the coop were small dowels, and the girls didn't seem to like them, so I replaced them with a piece of plank (about 3 1/2 inches wide), which they much prefer, especially the largest one, a Marans. What type of perches do you have? I found that changing to a wider perch made all the difference to their willingness to stay up there for the night. (And my perches are only 4 or 5 inches higher than the nesting box!)
Now that the colder weather is here I have put shredded paper on the floor of the coop for insulation (I only have a mini coop - rabbit hutch style - and I clean out the poop and any wet or dirty paper each morning.) From time to time one or other of the girls decides to sit on the floor for the night rather than perch. I can only assume that they have their reasons, and since they don't seem to get any more mucky than if they perch, and the floor is quite well insulated, I don't bother to move them.