Heatsink paste is used as an interface between heat sinks and heat sources. An example of a heat source is a LED component, that often creates and suffers from heat. So it is imperative to lead the heat away from the component. This is only possible by using IMS boards (ALU) and mount it on an heat sink using heat sink paste.
With a more complex layout, one can no longer rely on the single sided IMS but will need a double sided board. Heat sink paste allows to do that. Under the specific component we place a via and fill it with heat sink paste or thermal conductive and electrical insulated paste. The paste in the vias will lead the heat through the vias to the other side of the board. Here it comes in contact with a heat sink. We often use his type of technique for pulsing LED (examples are warning lights on emergency vehicles).
Our Design Guidelines have a section on heat sink on page 21.