Heat rises, so put the intakes at the bottom and the exhausts at the top.
It's generally cooler at the front of a PC (they tend to be accessable at the front, bu the rear is usually in a corner), so again the intakes at the front, and the exhausts at the rear.
Larger fans shift more air for less noise, especially if you have a setup which can control the speed of the fans based on the case temps.
Where possible keep the same amount of air (or more) being pulled in as being pushed out. Less intake than exhaust will cause a slightly negative pressure, so the difference will mean that dust gets sucked in the dozens of little gaps in the case. Keep in mind that the PSU fan might be an intake, so add that into the bargain.
Ideally, make sure one intake is over the CPU area, and ideally another near the HDDs.
Don't leave the PC in direct sunlight. If possible, have a window vent open to let out the heat.
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