The little 6 week old chicks are making their favorite hangout inside of the nesting box. They have plenty of places to get elevated and roost but, they seem to be roosting on a board that separates the nesting box from the main coop room and are leaving their poo in the nesting box. I'm new to raising chickens and am wondering if this is going to backfire down the road when they're ready to start producing eggs. Should I leave them be?
Should I break the habit or is this ok?
I would probably rearrange things. You are not going to want poopy eggs.
Maybe hang a roost bar just below the nest boxes and out a ways. They can use it to jump up to the nest box and if they roost there it's not in the nests. You might also want to cover the nest box area till they are old enough to use it.
Chickens normally like to sleep on the highest thing available, but normally doesn’t mean always. It sounds like your roosts are higher than the nests so they will probably eventually migrate up there. But what to do in the meantime?
They are not going to be laying eggs anytime soon. You need the nests open when they start to lay or else you will teach them to lay somewhere other than the nests. Then you have a bad habit to break. It’s possible they could start laying at 16 weeks but that is really early. Most won’t start to lay until a month after that, if then.
I’d block off the nests so they can’t poop in them and probably so they can’t roost there if I’m visioning your layout correctly. Make them find some other place to sleep. At their age it doesn’t matter that much where it is. If they are not sleeping on the proper roosts by 14 weeks of age, I suggest you start setting them on the roosts after it is too dark for them to get down. They should catch on pretty fast. Your ultimate goal should be to have them roosting on the roosts and the nests open at 16 weeks of age. Until then, don’t stress about it. You don’t really have a serious problem.