This ^^^I don't think chickens bond and form tribal units in an enclosure. Shadrach was talking about totally free range birds over a much greater area than a back yard. In an enclosure, you are very apt to get cockfighting, over-mating and abused pullets.
To the OP - do not get rid of all the little coops - they will be perfect for separating your cockerels from the pullets, which in about a month you will want to do. You will be very hard pressed to keep all those rooster chicks.
A picture of your set up would really help. And as AArt says where are you at in a general way also influences advice.
But to solve the immediate problem, I would just go down at dark, after they have roosted, and put half of them in the other coop. It really does not matter which ones, or even the same ones each night, just half of them. Do that for two or three days. Then at near dark, shut the gate with approximately half on one side and half on the other. At least some of them will have spent the night in each coop and the others will follow them in when there is not another option.
Unless you are in the Deep South, without winter, how they use the coop will change with the seasons. The amount of time spent in the coop changes dramatically with the long nights of winter.
Mrs K
