There were two different options I considered. Since my skirt was straight with no gathers, and the lining and skirt were exactly the same size, I just treated them as a single piece of fabric. I figured it wasn't really different than the bodice, which was underlined. I basted the two pieces together first -- machine basted about 1/2" from seamline and then did an overcast stitch on the edges by hand. (Just to the point right below where the zipper went).
Next I installed the invisible zipper. I placed the stop about 7/8" below the upper edge of the bodice, but should have done a full 1" as it was a little tight to get a hook & eye sewn on afterwards. I hand baste the zipper first to make sure it's lined up right, particularly on the second side. (After the zipper is in, I machine stitch the tape to the seam allowance to keep it flat, and remove the basting stitches.)
After the zipper was sewn in, I placed the bodice lining on top of the bodice, with the zipper sandwiched in between the two. This allowed it to act as a facing, and give a clean finished edge on top. I sewed the top bodice seam, then trimmed and understitched it. After the understitching, I machine sewed the bodice sides. This eliminated the need to tack them down by hand afterwards.
I have pictures if this explanation isn't clear -- I've started taking pictures of things I do since I have such a horrible memory!
The downside to doing it this way is the finish wasn't as clean on the skirt portion of the zipper since the lining was sewn to it with the fabric rather than tacked down afterwards. (I clipped the lining at the bottom of the zipper sew the remainder of it could be sewn separately and with the seam allowance to the inside.)
The other option was to attach the bodice to the skirt, but not the lining. Sew the bodice and skirt lining together, but keep the separate from the garment at this point. (The back seam on both is still unsewn as well.) Next sew in the zipper. After the zipper is in, then sew the upper bodice edges of garment and lining together, still sandwiching the zipper edge between the two. Trim and understitch edge. Fold lining over and tack edges to zipper. The advantage to this method would be the cleaner finish along the skirt portion of the zipper. It would also eliminate the need to hand tack the bottom edge of the bodice lining to the waist seam, although it would probably be best to sew a few stitches anchoring the two together at the seams. I already had the bodice sewn to both the skirt and the lining before I thought of this option, or I might have tried it this way.
I like the hand pricked zippers, but for a formal I prefer the look of the invisible zipper. I've never had one break, even on RTW garments, but possibly that's just been good luck!