Hey, GK. You have to match them. Usually, if you're going to lap your CPU then it's a good idea to lap the heatsink/waterblock as well. This way, you ensure that both are flat and will have optimal contact.
To test, take a straight razor and hold it against the base of both your CPU and the HK, and see if you can see any space inbetween the edge of the blade and the base of the heatsink/IHS.
Also, if the MX-3 is anything like the old Arctic Silver, you're not supposed to spread it yourself. Arctic provides specific instructions on how to apply it based on whether you have a dual or quad core. You're supposed to line it up over the cores:
http://www.arcticsilver.com/arctic_s...structions.htm