There are some very good tutorials on how to lap an HSF, which is really the same concept. However, I'll try to sum it up.
Use a very flat surface. A piece of plate glass (such as from a window) is very flat. Don't use concrete or your kitchen table. Those aren't flat.
Put a piece of sandpaper on the glass and tape down the edges to keep the sandpaper from moving. You will want to start with coarse and move to fine sandpaper. Each stage should be a finer grade of sandpaper. I can't remember the numbers for what you start and what you move to, but you should spend a bit of time with each grade of sandpaper before moving to the next. The first grade of sandpaper should make the waterblock completely flat (which means not bowed or cupped) although it will be a rough surface. Then, each successive stage should make the surface more smooth.
Use a black marker to put an X across the waterblock bottom for each stage. This way, you know when to move to the next type of sandpaper, and you will also know if you have an area on the surface which is not being smoothed out. The X should be gone before you move on to the next grade of sandpaper.
Alternatively, take your waterblock to a machinist and tell him to take a couple of thousandths off the bottom with his milling machine. That will make it very flat!
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