You need a lot of hideouts, and you need a lot of space. Both of you are talking a fair size flock. What seems like a lot of space now, may rapidly get to small as they all get to a mature size.
However, to your question, you need to split off an area in your run. Using the brooder that you are all ready using can help, as chickens don't like change. If you are using a box to contain them, tip it on the side and place it in the run. Have the run sectioned off into two parts, so all the chicks can see each other but are separated.
After a week or so of this, open the dividing fence so as it becomes a one way gate, in which the smaller birds can get through it, but the larger birds cannot. This allows the smaller birds to explore but have an escape.
Mrs K