Honestly, just do it like this.
Fill in the gaps between the Heatpipes and fins. I rubbed it in to the gaps very well to make sure there were no air pockets. ( Any air pockets or tiny bubbles between CPU and Cooler can greatly affect results.)
Then wipe off any excess leaving only the TIM between the heatpipes and aluminum fins, then apply to to HDT Cooler as shown in the link. And Pic from link. Link again
One last thing. Prior to application make sure the HSF and CPU are clean. To do this use Isopropyl Alcohol 90%+ pure (This is available from the chemist Drug store, and is very inexpensive.) or something like Arcti Clean and a lint free cloth or coffee filter paper. A clean HSF and CPU are very important for best performance. Good luck.