You probably already have several other fans. Typically the PSU fan is an exhaust fan - it draws air from inside the case, and vents it out the back. The GPU is usually set up to exhaust some air out the edge. And some cases let you place a duct over the CPU which turns the CPU fan into an exhaust fan.
So generally, if you're adding just one fan powered by the motherboard, it should be an intake fan so you're not fighting these other fans. Inflow is generally preferred since it creates positive pressure inside, meaning the dust buildup only happens at the intake fan(s). That makes it relatively easy to clean. If you have negative pressure, the dust builds up at every nook and cranny of the case.
Beyond that, you need to look at what the airflow will be like inside the case. Try to assure the intakes and exhausts generate a simple and orderly flow of air. No sharp bends, no air coming in one spot and going right out an adjacent spot without cooling anything. The flow should be over cooler components first (hard drives, motherboard), hottest components last (CPU and GPU) before being vented out of the case.