Yes you should they need air circulation. And you can keep those fan leaves just cut them in half to reduce transpiration. Rooting can take 5 days to 2 weeks depending on where off the plant they came from in terms of lower, middle, or upper portion of plant. Also, factors like humidity ( ideal is 80-90%) temperature actually underneath the clone tray and not the ambient temperature will stimulate faster rooting. Also, the type of rooting hormone you used could play a vital key in root growth.