There are a few places in Wilbur where you want to specify the map edges in degrees of latitude and longitude rather than as arbitrary units (e.g. the V2 shader). For those cases, the Vertical Scale control on the Heightfield 3D Preview window is useful for adjusting the heights down to reasonable-appearing value.

If you need to adjust the altitude to get a particular altitude at 0, the Filter>>Mathematical>>Offset filter will add a particular value to every sample on the surface (e.g. to move everything down by 23 units to flood a bit of land, use the offset filter with a value of -23). To scale height above zero and/or below zero to a precise range, use Window>>Histogram to find the current surface minimum and maximum. Use Select>>From Terrain>> Height Range and specify a low of 0 and a high of 100000. Then use Filter>>Mathematical>>Scale with a value of (desiredMax/currentMax calculated via some external program such as the Windows calculator) to scale the above-sea levels. Repeat, selecting a height range of -1000000 and 0 as the min and max, then scale by (-desiredMin/currentMin).