The aim here is to sandwich thick thermal pads under you MacBook's heatsinks to contact the upper case, and atop them to contact the bottom cover. This will help conduct heat away from the machine by effectively making the entire unibody one big heatsink.

On my machine, a mid-2010 15 inch MBP, I needed to use three strips of a 2mm thick thermal pad under the centre heatsink, two strips under the side one and one strip atop each to make contact with the bottom cover.

Try to use enough layers that the heatsinks are in good contact, but not so many that anything needs to bend to fit back.