IMO -
It is better to have a balanced intake and exhaust arrangement. This will ensure that the fans aren't working to pressurize the tower, but equally drawing air in as well as removing warm air.

Ideally, your intake fan should be at the bottom of your case as to ensure the coolest intake air. (if you're ever worked at height on lighting or other cable runs, you'll know how much hotter it can get within a 2 foot distance, HOT AIR RISES). Furthermore, ensure that your exhaust fan is at the rear and top of the enclosure, this will ensure that the hottest air is removed from the case and directed away from the intake location. You don't want to recycle already warmed air back into the thermal management system.
If anything, I would have more intake air than exhaust, at least that way the enclosure has positive air pressure and is less likely to draw in debris, dust, hair, etc. ... But this just a personal preference as I have animals in the house...
Ideally, balance your intake and exhaust, and ensure optimal air flow over your devices (CPU, video card, RAM)....

Hope this helps!
-KB