Where you place your seams depends somewhat on whether you plan to quilt using a sit-down machine or a frame. With frame quilting, you want to be careful not to have your seams running up and down as the extra fabric in the seam rolling upon itself will eventually distort the quilt.
Traditionally, the method is to run the full width of fabric down the middle with a seam on each side. This works well for hand quilting and also for machine quilting on a domestic machine. You can do the same for a quilt that will be longarmed, but in this case you would want to run the full width of the fabric from left-to-right so the seams aren't rolling on top of each other.