When I put an invisible zipper into a garment, i like to first machine baste the zipper - both sides, using a thread in the needle that is a slight contrast to both the zipper and garment. Then I check the look of the zipper on the outside - make sure it is just right. The contrast color thread makes it much easier to remove or pick out if necessary, particularly on dark colors. Then when I do the final stitching I use the matching thread - going just inside the basting thread.
see photos and more description on this blog post