Don’t split your planar surface with the circles. First check (with Dir) if the surface normal is facing “up”. Then just ExtrudeCrv the circles to the correct height (Solid=Yes) and use BooleanUnion with the extrusions and the surface.
Or, if you have split the surface, use UntrimAll on the base surface to “unsplit” it, then ExtrudeSrf (or the Gumball extrusion handle) the circle surfaces to the height you want and BooleanUnion.