It really depends on whether this will be quilted on a frame or not.
If quilted on a frame, the traditional method of splitting fabric so you have a large piece in the center and a piece on each side of the center is not good. This is because the seams starts to "pile up" as the quilt is rolled, creating bumps where the extra fabric of the seams are. In this case, it is better to have the seams running from side-to-side rather than the traditional up-down.
If quilted on a domestic sewing machine (or a sit-down longarm), which direction the seams run doesn't matter as the quilt is not rolled onto a roller as you quilt. Whatever looks good works!