You always want to pull air out, that is an "exhaust fan" and will always make for better circulation. When the fan is pulling air out of a space, it is creating a vacuum and will allow air to be sucked in (from somewhere, more later). Pushing air in will only pressurize the space not allowing the hot air to evacuate the space as quickly thus slowly heating up the space that you are trying to cool.
You also dont want the intake and exhaust right next to each other as it will just suck the hot air right back in and pull the cold air right back out. If the intake and exhaust are going to be in the same window, install some type of divider between the 2 that extends at least a foot. In a perfect world you would want 1 intake fan and 1 exhaust fan in 2 different areas of the room. But if you only have 1 fan then blow the air out and open a window that is close for fresh air. Even just a crack will help. If you dont you will be sucking air from the main house, even with the door closed (unless its a sealed exterior door), and in the winter time you will just be blowing wasted gas heated air outside. Or do like I do in the winter time and reconfigure the fans and let your rigs heat your basement thus helping to heat the rest of the house.
To get back to the op question, 1 blowing in and 1 blowing out and the rig somewhat close to the exhaust fan. Or 2 blowing out if there is another window you can open to allow air flow. Whatever way you do it, you always need the air that is being sucked out to be replaced with the same amount of air that is being sucked in from somewhere, via the main house or a window. Quick and simple example without going into formulas and such: 1 gallon of air being sucked out needs 1 gallon of air being brought in, thats a 1:1 ratio. 1 gallon being sucked out and .5 gallon coming in = 1:.5, not very efficient. 1:2= over kill but way better than the last.