Just cut a hole that fit the "waist" of the bottle; then open the cap and slightly crush the bottle so as to squeeze it into the hole.
This is how it looked inside the box as I tried to achieve darkness by putting my hand with the camera inside the box and then tried to wrap the flaps around my hand but the result is not optimum.
So I figured out a way by opening a small hole for the lens of my camera to shoot inside from the outside of the box; this way, the box would be darker and the light should be more pronounced. By the way, I did closed the flaps/lid of the box when I shoot the photo.
Another problem come out in that by this time, the heavy bottle filled with water could not be held by the box as the hole had became larger and lost its grip. So I decided to use a thick slab of styrofoam as a neck which did the trick. There are often challenges and problems that crop up during experiments and one must try to overcome such problems to achieve our objectives.