Try and think about how air will move in the case. You aren't just cooling the CPU and even providing air to the GPU 's fan system, you need to move air over the motherboard and even your hard drives. Your PSU may also need air.
What are the points of entry to the case, even if they don't have fans. Are there vent grilles on the front and sides? If plenty of vents then your top and rear can probably both be exhaust as the air will get drawn in elsewhere. But if the front is effectively sealed then that rear fan should probably be an intake.
Some software can help you monitor temps on certain parts of your PC. That may help you find the best arrangement of fans, and their speeds.