You want a natural airflow flowing through your case, from front to back.
Most cases come with 1 fan on the front pulling cool air in. A second fan on the rear pulling the warm air out. In addition, all CPU's today need cooling blocks, and those have a fan to move the heat away from the CPU, and heat always tries to go up. Most video cards also come with fans, and most of those push at least some of the heat from the card out the back of the system.
I personally like a to try to have a positive pressure inside of my case. What this means is that you have 2 fans on the front pulling air in, and still only have 1 fan on the rear. This helps a little to keep dust out, but mainly, it pushes even more cool air through your case.
Adding fans in other places is not generally helpful, because they disturb the natural front to back flow of air, and that can create pockets of hot air inside of the case.