For hand quilting I like to stitch in the ditch on the side without the seam allowances. If your fabric closely matches the thread you used to piece with, you could press the seams open. You will be quilting through the layer of fabric in the top, plus the seam allowance fabric if you stitch in the ditch though. If the piecing thread is a contrasting colour, when you hand quilt, the stitching will pull the seam open a little so you will see the thread. It's your quilt and you can do it the way you are most comfortable with.