There are several ways, maybe one will look good. I can think about these ones, from top of mind.

You could try to select "decay near foreign objects", with a small number (say, 1% or even less) but if the size of the stones is small (compared to the grass) that will not work properly. You might have to use the eraser in the eco-paint dialog, after populating, to delete some invading grass blades.

Another method could be to boolean subtract the 4 cubes from whatever you have as ground. In this way, there will be holes in the ground in the place of the cubes and so the grass won't populate there.

Yet another method is to create a bitmap to work as distribution map. In this bitmap, you would put black areas where the stones are and white everywhere else.
To create the distribution map, you could do a render from the top camera and use that as a basis for your design.

Hope one of these will help.