Gathering stitches and seam allowance

I'm working on the fairy tale dress now and am completely confused about the instructions for the gathering stitches for the skirt and sleeves. The pattern calls for two rows - one at 3/8 and one at 5/8". But then the seam allowance used to sew the skirt to the bodice and the sleeves to the bodice is 1/2". So the gathering stitches at 5/8" show through. What am I doing wrong? I've read and re-read the pattern and I can't figure it out. Thanks in advance for your help!