PCB Solutions, a provider of high quality circuit boards, has a great post on if conductive or non-conductive thermal epoxy should be used for PCB’s needing filled vias.  We’ve expounded on the benefits of including your PCB design and layout as part of your overall thermal management approach here at our blog. It’s important to do so as including thermal management into those designs might even remove the need for you to have heatsinks at all.
We’d highly recommend reading PCB Solution’s post, “Conductive vs. Non-Conductive Via Fill“.