A dog crate and a saftey zone. A temporary fence for a couple of days, then lift the fence off the ground a few inches as a saftey zone whereas a chick can escape back into, feed them in that.
If you are very tight on room, you need to be extra careful as tighter areas can cause more violent behavior.
If you can't add another fence, I have also turned out into the yard or free range the hens, locking them out of the set up. Then lock the chicks inside the coop/run. Feed along the fence. This lets the chicks explore the coop without being chased for their lives. Now you can put the chicks in the dog crate or box for the night, where ever you have them now, for a few days, wash and repeat, and then let the hens into the chicks in the run very close to dark, make sure the chicks have a lower roost, aways from the hens in the coop.
Add a bunch of clutter, hideouts, escape routes, platforms, roosts inside the run and mulitple feed stations are other tricks that help.