front- fits a 120mm (and 80mm but mine are two thick to go in the front but the 120mm fans fit fine)
side - fits 2 80mm -120mm one above CPU and the other above PCI slots (almost)
back - fits 80mm- 120mm
top - 2 spots, one above the CPU heatsink and the other above the RAM fits 80mm-120mm
currently i have 2 120 fans on the side and one 120 in the back then 2 80mm on top
eventually ill have them all be 120mm and really loud!! thats right loud, just how i like it!
Air goes in the front, out the rear.
Air goes in the bottom, out the top.
Try to keep airflow in 1 direction only. Either front to rear or top to bottom
Watch for dead air spots that trap heat.
Try to equalize in-flow with out-flow. If you have 120 fan going in, make a 120 fan go out too.
Beyond that, using a fan controller to control your fan speeds sounds like something you should read about. Also, you probably are not using the best fans anyway. You should read up on the specs of your fans and how to use that to the best of their abilities.