Understand what CR-10S fans are cooling
Photo Credit: Courtesy of 3DStockPhoto ( image)

The function of the front fan is keeping the cold end well... cold. :) It should be spinning as long as the printer is turned on.

The right fan is known as "part fan" and its function is to cool down the plastic that has been just extruded, the idea being to solidify it as soon as possible. As you noticed it is controlled by the gcode and it can be turned on, off and even made spin at any speed in-between still and full throttle. It normally stops spinning at the end of the print (with some plastic like ABS it may be set not to spin at all even during the print).

If you take a closer look at your CR-10, you will see that the receptacle the air is blown into by the part fan has no bottom: that slit is where the air passes through, before being deflected 90° towards the nozzle.

On the CR-10 the standard deflector for the part fan does not do a good job (the air is not blown where it should) and replacing it with a custom part is one of the most common upgrades performed on the printer.

Personally on my CR-10 I used a custom mount with an integrated "fang" that blew the air from both sides and worked really well. It also had the advantage of reusing the hardware from the original assembly (= you don't need to buy anything, just print the part).