Before getting into details, your room temp has a lot to do in terms of your cooling performance. This sticky from the CPU forum has a lot of info regarding cpu temps, you can read it later if you want:
http://www.tomshardware.com/forum/id-1800828/intel-temperature-guide.html
Regarding the CPU cooler, from what you've said, the issue is that it is fighting for air with the top-rear exhaust. rear[<--.......|cooler| -->..............]front
( "<--" represents a fan and it's direction )
So while it's not ideal for the hot air to move towards the front of the case, the bigger issue is that it's not getting unrestricted fresh air at all. Say you were to flip the top rear fan and make it an intake, then your temps should go down.
Better way to set it up, IMO, is to leave the rear exhaust alone, switch he cooler's fan to a pull on the other. Then place an intake fan on the top so that it blows fresh air into the side of the cooler.
_______________\intake/_
[<--.......<--|cooler|..............] front of case
Or this other way, but then it will not be ideal with a open cooler type of graphics card.
______________________
[<--.......<--|cooler|<--.........] front of case
Regarding the side fan, that be quiet! case has it right in the middle. (or so it seems) So check were would the air flow go to when there is a fan there. As in, does it conflict with the gpu cooler fans or not.