Use a top and bottom of job setting. Be careful to note that the z level rough is looking at the "material to remove" and not the surfaces being machined. The toolpath will not make an extra step at a "lessor than step down value" to reach the "bottom of job" setting, so the next tool may have a bit more than the defined step down, unless you set the tops and bottoms to match the step down increment amount. Some imported 3d solids will carry "bounds data", somethiong like .002, so this has to be accounted for when setting your tops and bottoms correctly on the first passes.....
Also, rule #2.... Dont mention Z-level rough anymore. Use advanced rough.