The basic idea, bring in cold air and exhaust hot air. I always do the math and add the CFM coming in and the CFM coming out. CFM = Cubic feet per minute.
Setup? Basic rule of thumb for people with low experience go with the "golden" method.
Intake in the front/side panel
Exhaust out the back and top
Personally I keep the "positive pressure" rule in work in my machines. When building your system it's a must to have good ventilation. However, ventilation causes air movement which brings dust in and dust = heat over time! So the idea goes back to adding the CFM in and CFM out.
If you have 200CFM coming in and 200CFM going out, you're pretty much at neutral pressure. This simply means the air is being evacuated at the same rate as it's coming in.
If you have 200CFM coming in and say 250CFM going out, you have negative pressure. This means the exhaust fans are actually pulling out air faster than the intakes are pulling air in. Now, this is why I keep positive pressure. When you run with negative pressure, your case which isn't sealed will have air coming in from everywhere which can actually cause more dust to enter the case and even disrupt a good airflow.
If you have 200CFM coming in and say 160CFM going out, you end up with positive pressure. This means the intake fans are bringing in more air than the exhaust fans can push out. This causes air to leak out of the crevices and small spots that bring in the dust during negative pressure.
Now I never go with an extreme positive pressure but I try to keep it about 50 or so CFM higher on the intake side as my case is WELL ventilated. Over two weeks I have had next to no dust enter my system since my last cleaning. Positive pressure does help as before I had a more neutral setup and would have to do cleanings once a month no matter what. (The underside of my desk is a certain dust magnet for some reason?
Anyways, take account of every fan, make sure your cabling isn't disturbing a lot of the cases airflow and just use your head. Look at where the air will go from the fans. Where will this fan push the air into my case to? Will this exhaust fan pull all of the hot air coming from my processor?
I personally have my PSU taking air from inside the case as my tower is on a tray on the carpet floor. However, I have intake fans blowing towards it and one right in front of it. Either way, just use your noodle. It's not rocket science when it comes to realizing where the air will end up. And seriously take the time to do the math and figure out your CFM. It may only net you a little less dust and 1C in temperature difference but it could end up saving you 5C inside the case!
I hope this helps you out amoguy!