Once you have seen what size and connector type fans will fit into your case, the next step is to look at how the fans pushes air through it, and where to positions the fans.

There are 2 different kind of fans when it comes the the physical wind that they are creating. SP and AF Fans.

SP-Static Pressure
AF- Air Flow

SP fans are used when the airflow is restricted such as a radiator.
AF Fans are used for pure airflow and when nothing is restricting the airflow.

So if you have a watercooler, then preferably put SP fans on the radiator.

The next step would be to choose the amount of fans and orientation.
Now this is where lots of people differ.

To create a Negative or Positive Pressure System.

In a Positive System there is more fresh air coming into the case than there is hot air exiting the case. Basically, the CFM from intake fans exceeds the CFM from exhaust fans.

In a Negative System there is more air exiting the case via exhaust fans than fresh air entering the case via intake fans and vents. The CFM for exhaust fans exceeds the CFM from intake fans.

(CFM= Cubic feet per minute)

I personally have a balance usually. Currently I have a Push pull Rad with 4 x 140mm fans as an intake and then 4 x 140mm fans as exhaust fans at the moment.

As a rule of thumb hot air rises and thus will be much easier to pull the hot air out through the top.
Generally pulling in fresh air from the front, and then pulling it our from the back and top works the best. BUT this is not the case for all cases, there are exceptions but these are very few.

Having a positive and negative system also has an influence on the amount of dust build up in most rigs. I have experienced with my case that a Negative system keeps the system a bit cleaner than a positive system. This also depends on the specific build but remains a general rule of thumb for me.

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My PC showing the 3 x top Phanteks 140mm Exhaust Fans, 1 x Back Phanteks 140mm Exhaust Fan, 2 x Front Intake Phanteks 140mm Fans on top of Rad and then out of sight are the 2 extra 140mm intake Fans.