WTF, just lost lengty post trying to submit it:(.
Anyway, would recommend the top fan to blow air out, as the air is the hottest there. You don't want to work against the free raising hot air in your table. Your cold air intake should be the closest to the floor, as it's the coldest there. You could use both fans to blow out, as long as you have some intake holes in your box, but what's the point of sucking colder air out from the bottom anyway?
If you would go with the bottom fan as intake, you could try using a mesh filter (looks bit smaller than the stuff on screen door or similar). I have that in my Antec P-160 computer case and it works pretty well. Have to clean the dust from it every month or so. The more/bigger fans you have the lower rpm you can put them on, resulting in less noise. Good quality/quiet fans cost bit more, but are worth in the long run. The same with quiet power supply. Constant hum from all these noisy fans is definitely annoying, so this would be money well spent.
Mark