Go ahead and install the top fan as exhaust, and switch the side fan to exhaust. You want to try and remove as much warm from inside the case to the outside. Think about it, you have at least two fans pushing cool air into the case but only one removing the warm air out. You want to get that warm air out from the two cpu fans, you do not want to recirculate warm air.
the 2 cpu fans are pushing then pulling air through the back though, I have a fan in the back exhausting the air that is pulled through the 2 cpu fans