I always 'lap' my HSF and core before applying compound. I start with something like 800 grit sandpaper and work through the grits I have to something like 1800 and I then use the back of the sandpaper and wet sand both the HSF and heatspreader (if it's a P4) and polish them both until they are like a mirror. If you sand the heatspreader on a P4 down enough, it has copper under there which will transfer heat to the HSF nicely, but it isn't necessary to sand down that far.
Then I take a plastic bag, put my hand in it and put a bit of paste on the end of the bag/my finger and wipe it on the core or heatspreader then I use a blade to smooth it out. The idea here is to make the THINNEST layer possible... the thinner and smoother the better. I work on mine until it's perfect and thinner than a sheet of paper. Then I take the plastic and rub a bit of compund onto the bottom of the HSF to get the compound into the metal on the molecular level and just keep rubbing it into the bottom until it's just foggy, but don't use too much on there.
Now seat the CPU and install the HSF.
That's how I always learned to do it and it has never failed me.
