OpenSCAD: Add spheric indents to a box

I created a box using "boxes.scad". I subtracted a slightly thinner box to create a hollow one. Now i want to create spherical indents on the box (see picture), but if i subtract a sphere from the box i just get a hole. How can one create the indents like in the picture?

If I understand your problem correctly, what you have now is on the right of this image and what you need is on the left :

Then what you can do is to subtract a slightly bigger sphere from the slightly thinner box before doing the main subtraction. Here is an example of what I mean :

a = 16;
b = 1;
c = 12;
d = 6;
difference(){ // main subtraction
    cube(a, center = true); // slightly bigger box
    
    difference(){
        cube([a - 2 * b, a - 2 * b, 2 * a], center = true); // slightly thinner box
        
        translate([c, 0, 0])
        sphere(d + b); // slightly bigger sphere
    }
    
    translate([c, 0, 0])
    sphere(d); // slightly smaller sphere
    
    translate([0, a, 0])
    cube(2 * a, center = true); // cube that hides half of the result just to see better
}

Note that the two spheres have the same translation and the difference between their radii is simply the thickness of the wall.