i usually just left the water changes till they were free swimming, then i would take water from the surface from the opposite side of the tank they were on, i think you could just take water from the compartment thats seperated off cause it wont upset the parents that way, also only do small water changes as the babies wont like it if something changes suddenly, so id say 10-15% at most every 3-4 days , and keep up the good work