The most important thing to do first, is to make sure both rails on each side of the table are parallel to each other. If they're not, your spoilboard will never be flat.Do you guys shims your table and spoil boards?
If the rails are parallel, then you surface the spoilboard to make it flat. Don't bother shimming .01, just route off the high spots. When cutting your parts, it's common to cut up to .01 into the spoilbard to make sure you cut all the way through your material. When the spoilboard gets a lot of cuts in it, you just remove another .01" to get it smooth and flat again.