being a long arm quilter i always ask that backings be peiced horizontally- that way when the quilt is loaded on the frame the seam runs evenly along the length of one of the bars...if the seam is vertical then in the center of the quilt, with each turn of the bar you build up 4 layers of fabric- in just a few turns you have very baggy/loose side edges because of the bulky buildup in the center.
if hand quilting it does not matter- and i don't know if it really makes a difference when using your domestic machine- but it makes a huge difference if long-arm quilting