It really depends on the width of your batting. If you have very thin batting, you might want to sew with a 1/2" seam. If you have mid-loft batting, you might want to sew with a 1/4" seam. If unsure, create a sample quilt sandwich, sew on a scrap piece of binding, and see if you can turn it to the opposite side and have the turned binding end where you want it.
One thing to keep in mind if you plan to miter the corners (which is what most quilters do) is that you *must* stop your seam the same distance from the edge as the width of your seam allowance. If you sew a 1/4" seam, stop sewing 1/4" from the edge in order to have a good miter. If you sew a 3/8" seam, stop sewing 3/8" from the edge. If you sew a 1/2" seam, stop sewing 1/2" from the edge. Otherwise your miters will not work out.