Elevation is a less important attribute of Road types: it had no affect on routing.
In most cases the elevation should be defined "as is" in the real world. Standard "Ground level" or 0 or in case of a cross-over / fly-over the upper road should be defined with an elevation one higher. In case of a tunnel the elevation could be -1 or -2.
One exception: the elevation of railroads should be set at -5.
See also the global Wiki page on Overpasses, Underpasses and Bridges.