One side of the thermal pad is slightly 'tacky', the other side has a removable plastic strip/film on it that protects the 'sticky' side of the thermal pad. You'll know which side is which since as soon as you take off the strip/film the damn thing sticks to anything it touches.
The 'tacky' side goes against the SSD, the 'sticky' side goes against the heat sink. I used both thermal pads on my PX1, one under the SSD and one on top of it. The one under the SSD should be stuck to PCI-e card, within the markings/lines that are provided.
So....the short answer to your question is that there is only a strip/film on one side of the thermal pad that needs to be removed.!