Hi Andrew,
The way I have got the best results is like this.
Fill in the gaps between the Heatpipes and fins. Rub the IC Diamond in to the gaps very well to make sure there are no air pockets. ( Any air pockets or tiny bubbles between CPU and Cooler can greatly affect results.) Also warm up the HDT Cooler and the IC Diamond so they are easier to work with. This allows you to work the thicker compound into the gaps more effectively. Otherwise it can be a little hard to make it stay between the pipes and aluminium fins.
Then wipe off any excess leaving only the TIM between the heatpipes and aluminium fins and perhaps leaving a very slight haze over the copper of the heatpipes.
Then apply to HDT Cooler as you do with all other coolers, a pea sized blob on the CPU. Or the 2 thin lines on the aluminium fins. Try both and see which works best for your setup. The blob has worked best for me.
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 Arctic Clean and a lint free cloth or coffee filter paper. A clean HSF and CPU are very important for best performance. Good luck.
The thin lines were difficult to do as the IC Diamond is as thick as it is but can be done if the compound is warmed up well beforehand. I also found warming up the CPU with a hair dryer just before applying the IC Diamond helped get a more even spread when attaching the cooler. But you may not want to put that in instructions as it may seem a bit too much work for some people.