Now, you should normally have replaced each thermal pad on your motherboard. You now need to replace your thermal paste (ARCTIC MX-6 in my case, for the same reasons as previously mentioned). This is fairly easy as you are simply required to deposit a single drop of thermal paste on both orange surfaces (i.e.: your graphics board and processor).

Once you have done that, you can either press down on said drop with a hard flat object to easily spread the paste on the surface (this step is recommended by ARCTIC), or you can let the heat exchanger press on it as you screw it back on. Please note that I only skipped that step because I did not own such flat item.