It sounds like you are hand quilting? When I used to do that, I did mark the entire thing first. But like you say, it's hard to keep the marks on there. So what you could try is instead of putting all the markings on first, divide up the space evenly, so you know which sections to stretch and which to squish. Then you can mark each section as you have been doing, but you know it will come out evenly.
For marking the divisions, maybe you could use safety pins (if they won't get in the way of the hoop), or what about just one or two stitches of colored thread (like a basting stitch) that can be pulled out when you no longer need it.
Andi