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I'm not really sure if you can do a "deep litter method" in a tiny little A frame tractor. I don't use that method myself (I use sand in my coop), so you probably better ask that question specifically in another thread to find out if you can do it in a tractor on such a small scale. I doubt it. The whole method relies on you being able to add layer after layer of shavings on top of the soiled shavings, but in an A frame tractor you'll run out of headroom after only a few inches. I think a poop board/tray might work better for you in this set up.
Yes, birds do poop all night (and all day, too, but during they day they're always moving around). They go to bed with food in their crops and their digestive systems continue to operate while they sleep. That's why a poop board or tray under the roost is such a great invention. All those droppings collect in one place and a board or tray makes removal quick and easy. You can do this daily and keep the inside of your coop nice and clean.
You don't want to confuse the nestbox with the poop tray/board, and you don't want your chickens to get confused, either. Make sure the nestbox is lower than the level of the roost and your chickens probably won't start sleeping in the nestbox. As mentioned before, you don't want them to sleep in the nestbox because of the poo.
Chickens prefer to dust bathe in actual dirt or sand. I imagine if they're deprived of a proper dustbath, they might try to use the shavings, but shavings wouldn't really do the job properly. Provide them a separate tray or bin with sand in it. They love it.