There is probably no reason to separate them, since they have all already probably been exposed to it. It sounds like mycoplasma (MG,) a chronic respiratory disease. The Terramycin eye ointment is good for chickens used in the eyes twice a day. Get any drainage off or gunk out of the eye first by washing with saline or water. Tylan 50 injectable given orally is good for treatment. Dosage is 0.2 ml per pound of weight given twice daily for 5 days. Encourage them to drink enough fluids. A little plain yogurt added to food twice a week can help while on antibiotics. MG is a chronic disease, may flair up again later, and the flock should be closed since they would be considered carriers. MG is common in backyard flocks.