I have been SO remiss on migrating salient posts from my (now shuttered) old blog to here, but I'm going to try to do better. And here is one that I use ALL the time.
When I'm making a garment that has topstitching along the fly or a mock fly opening, I trace the stitching line on a scrap of pattern tracing paper. Then I pin the template to the garment's front and stitch through the template along the marked line.
Once you're done stitching, tear away the paper and voila, a perfectly done topstitch! I like it better than thread tracing or chalk marks. It's easier to remove than the former, and doesn't risk brushing away like the latter. For me, it's perfect.
I've seen some plastic templates for marking your fly stitching. While I am a big supporter of creative sewing notions and their manufacturers, I prefer this. Plus, I can make one of these templates for literally nothing by tracing onto a scrap of pattern tissue.
I hope that helps, and happy sewing!