Hmm there are quite a few ways to apply the thermal paste.
Some people like to drop a pea-size amount in the center - then let the Heat sink do the spreading itself once you clamp it down.
Others like to spread it even with a credit card (this is what I did) over the CPU itself.
And don't be afraid to put thermal paste on your CPU, as long as you don;t put too much on, it should be good.
Heres a nice litte guide it's older but still works, I reccomend reading through them both:http://www.techpowerup.com/printarticle.php?id=134