Remember to keep positive airflow in your case, so you need more intakes than exhaust fans. As for your current setup 2 fans for intake and 1 for exhaust is a good ratio of intake to exhaust. I suggest for your new setup to draw in cooler air (intake position) for the side fan and exhaust out through the top of the case (exhaust fan) because hot air rises.
On another note, just remember the more fans you add to the case the more maintenance you will need to do because of more ways of dust that can build up in the computer which can actually lead to increased temperatures. Unless that case comes with built in fan filters, I suggest going out to buy a few for at least the intake fans.