This is how I apply thermal grease...
- put a
small amount of grease on the core itself
- grab any clean plastic bag (a grocery bag is usually handy)
- turn the bag inside out (the inside is usually cleaner than the outside)
- put my index finger in the bag and stretch the bag around my finger so the bag is really tight and is not creased at all
- using said finger I spread the grease over the core (going from the center out to the edge - to avoid getting grease on other parts of the CPU)
- rub whatever grease is left on the bag to the bottom of the water block (or heatsink - do people still use heatsinks???

) right where the core will touch it
- install the water block (twisting the block a little once installed)
Using the above method I have never had any problems.