welt here is what i do with all the computers i build
the top and back fans- exhaust
and the side window intake so it hits your GPU if you have one
as for a bottom fan i never needed to use that slot so i would say after setting up the way i described try both intake and exhaust on the bottom to see which is better
also if your power supply unit has a fan make sure you face the fan down so it can dispel the warm air out the case
also to check your temps use speccy
http://www.filehippo.com/download_speccy
speccy will tell you all your temps for CPU, motherboard, hard drives, GPU as well as much more
of course that's if u need a temp checker
let me know if that works for you