In my opinion, it depends on the tools with which you are planning to mark. I've used chalk products that were pretty much worn away during the handling process. Particularly on a large quilt like that. I prefer pencil marking and mostly mark as I go unless it's an all over design that needs to match up. Since that is not your plan, I would mark as I go.
I have one of the old style 'lap desk' things (hard top with pillow attached to the bottom) that I use while hand quilting. I mark as I go (with pencil) but have that under my work so I have a solid surface on which to work. I can then just lay that aside and continue quilting.