I've beeen playing about with planets and water. all I do is set the water sphere very slightly bigger than the terrain sphere.
Usually a value of about radius = "6.3783e+006" (red numeral is the one I've added to the world radius) seems to work. If things like shore line texture are then in the wrong place I'll raise or lower them proportionately rather than trying to get the water to a zero altitude. The biggest issue I keep running into is the the numeric feedback for anywhere other than the top of the world is pretty useless. Whats the point of knowing a mountain at the equator for example, that is clearly way above the water line is actually -1996m, everywhere on its surface, dont get it... :|
Richard