Aim to cool the entire lot with 1x120mm fan - Id suggest going CPU first, psu last, and whatever else inbetween
ducting is definitely the best idea, imo.
Where the heck would you fit a decent sized gfx card in that box? or is it open between two of the layers?
The size suggests its fairly small (looks to be about 50-70mm to be aesthetically pleasing, by the look of the cd/dvd slot you have on top)