I don't mind the pond looking empty and the way it is. With the way you've classed up everything around with flowers and garden stuff, it compliments the normal pond, since this pond has lily pads in it, which is something special with the house. If you want, you could try constructing a boat, or make the pond inaccessible to make it seem more special.

I still think the Graals stand out a little too much atop the house. I'd try something subtle, like hiding them around a bit and surrounding them with the flowers and greenery.

People will see them hidden around and still understand their significance.

Another idea would be to put the blue one near the pond, the green one around some interesting trees or flowers, yellow around some rocks, and red around a fire, torch, fireplace, or something warm or hot. Putting the Graals near their respectable elements really wouldn't be too difficult for blue, green, and yellow. With red, you may have to be more creative.