That's one of the reasons that I seldom look at pattern directions when sewing as there are so many steps left out. A lot of designers do not know construction techniques which is one of my pet peeves. What I do is to have the waist seam pressed to the skirt with a waist stay attached & I put in the zipper between the fashion fabric plus underlining with the lining next to the skin. A waist stay is something like grosgrain ribbon or hem tape sewn across the waistline to keep the weight of the skirt from pulling down on the bodice. Oh, how I wish you were closer so I could show you how to do this. Sometimes, I think that my explanations are inadequate. Remember, the skirt will be held up by the bodice & needs a little extra support. You treat the bodice & skirt as one piece of fabric when inserting the zipper. Also, use interfacing in your zipper opening. Some of the older sewing books has this information on how to insert a zipper between a bodice & skirt. I'll research some of my sewing books to see if I can find a clearer explanation on this. Don't be afraid of your fabric.
Brighten each corner where you are ... smile!