I have 4 fans running, one in the top, one at the back, cpu fan, and front fan, I am not sure if I connected them into the right fan headers, my motherboard is ASUS P8P67_PRO/
To be honest as long as your CPU fan is plugged into the CPU fan socket the others aren't that important. If you have 4 pin pwm fans they will work better plugged into 4pin sockets but the worst case scenario is that your fans might run at full speed and be noisy if they aren't in the ideal socket.
Save the money for a better GPU, that 560 is pretty long in the tooth by now. Another upgrade could be an SSD but its your GPU that will be struggling in the next year or so