It is so annoying that the comforter/bed spread industry has not increased the size of their products to match the increased size in mattresses. Because, you are right, the sizes are not compatible. They even are going as far to say that one size is for a full/queen, which is not correct as the full/queen size always falls short on a queen size mattress. Same with duvets.
Like "mereliz" stated, putting a fitted sheet on your box spring may be an answer to covering the box spring, but even still, that does not make the comforter fit any better. Perhaps a king size comforter is the answer for a queen bed.