I had the nest boxes in the coop from day one. Mine are inside with a door from the outside for the eggs and are about 10" off the bottom of the floor. The first night in, they all roosted on top of them. It was very crowded with six birds on a 12"x24" shelf. Since then, I put boards on top, leaning diagonally so they can't roost on it and set their roosts above the height of the nest box. I put some sweet timothy grass in the boxes, a couple of golf balls and left them. This was when they were about 10 weeks old.
They never went in there and messed it up or anything, but they free range in the back yard so they didn't get bored. I got my first egg about three weeks ago and it was laid (with encouragement) in the nest box. Now three of them are laying and they lay in the nest box. If you set your roosts high enough so they won't go and sleep in the boxes they should be fine. I have also heard that having the nest boxes on the floor may encourage them to scratch in them and they might break an egg and then become egg eaters. I don't know how true this is.
I would just put the boxes in as they will be when they start to lay so there's fewer changes they have to adjust to. If they get in them and become destructive, you can board them up until egg time. Good luck.
Mary