When you are sewing together pieces for a quilted garment, you should make allowance for the bulk of the fabric layers.  Seams should be sewn with an 1/8" allowance for the loss from "turn of fabric" when seams are pressed, as the heavier quilted fabric will not press as flat as a single layer.  That means that if your pattern's seam allowance is 5/8", and the garment is not intended for quilted fabric, sew the seams with a 1/2" seam.