Complex sentence: Eventually, as the Church grew, individual congregations no longer each had their own bishop, but the bishop in a large city would appoint a presbyter to pastor the flock in each congregation, acting as his delegate.
Split into simpler sentences: Eventually, as the Church grew, individual congregations no longer were served directly by a bishop. The bishop in a large city would appoint a presbyter to pastor the flock in each congregation, acting as his delegate.