I don't own a Prusa but I think the cooling fan is for cooling the cold side of the print head....and not for cooling the extruded plastic. Stopping that fan will stop the printer actually printing.
One cools the filament path and remains on all the time - otherwise the printer will stop working very rapidly.
The second one cools the surface of the printed part to quickly solidify the extruded plastic.
For PETG, you have a lot of things you can do with the second fan -
You can use a high fan when you need it to quickly solidify small details and bridges. However, running a fan at full speed all the time can reduce layer adhesion.
A low fan can be used to give you good layer adhesion while maintaining reasonable small detail assistance.
Anywhere in between changes the balance depending on the setting.
Turning off the fan completely gives you the best layer adhesion, but small objects or details may suffer if they retain too much heat.