What you're calling the roosting box is the coop. Then you have a small run attached to that, and what looks like a bigger run enclosing the whole thing.
The coop layout is the issue, that's why they're not roosting in there. Looks like you modeled this after many prefab style coops that are seen online? The problem is, you modeled it after pretty bad coops.
Roosts should be well higher than nests, not 1" off the floor. Coop also has almost no natural light and no ventilation (those tiny holes are woefully insufficient, you want to aim for at least 1 sq ft per bird of vents).
If you're fine with them sleeping in the mini run, then really don't have to change anything. Do they ever go inside the coop at all? Since the coop is dead space if they're not using it, I'd really be tempted to tear out the inside walls completely and just open it up for them to use the full space inside the mini run as their coop. Nests can be reused, probably moved down a bit on that wall.
The coop layout is the issue, that's why they're not roosting in there. Looks like you modeled this after many prefab style coops that are seen online? The problem is, you modeled it after pretty bad coops.
Roosts should be well higher than nests, not 1" off the floor. Coop also has almost no natural light and no ventilation (those tiny holes are woefully insufficient, you want to aim for at least 1 sq ft per bird of vents).
If you're fine with them sleeping in the mini run, then really don't have to change anything. Do they ever go inside the coop at all? Since the coop is dead space if they're not using it, I'd really be tempted to tear out the inside walls completely and just open it up for them to use the full space inside the mini run as their coop. Nests can be reused, probably moved down a bit on that wall.