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I agee with to this post. I'll repeat some and add a bit more.
Make sure your roosts are higher than anything you want them to roost on or in. Make sure they can get to the roosts. If they are too high, they may need a step, perch, or ladder. With 12 chickens and the usual recommended ratio of 1 nest box for 4 laying hens, you do not need the top ones. If you can, I'd suggest removing them instead of just blocking them off. I don't like having any space the chickens cannot get to in the coop since it may give mice a place to nest.
I also suggest blocking them off after you make sure the roosts you want them to use are the highest possible roosting areas in your coop. They are creatures of habit, so if you can get them used to roosting where you want them to, you are likley to do OK, especially if it remains the highest place in the coop. Somewhere around 16 to 18 weeks of age, open the nests up and put a fake egg in there to show them where to lay. They probably will not start to lay that young, but they might. You do want them to start laying in the nest boxes. They are creatures of habit and if they start laying somewhere other than the nesting boxes, it can be difficult to retrain them.
I think it is a good thing you found out you have a problem before they started to lay. You have time to correct it. Good luck!