Hi there, good for you on breaking out of your box! : ) I usually mark my quilt top before I sandwich it because I thought that it would be easier to mark if the top had a hard surface right behind it- then, on my current full-size top, after I spent three days marking the entire thing, I sandwiched it together, started quilting and... all of the light marks had completely disappeared! I was so frustrated. Now I'm marking a section at a time as I go and it's working fine. Now that I've said all that, I was going on the assumption that you are hand-quilting it? That's what I do; I don't know if it matters if you're machine quilting it.
As far as what to mark with, after that fiasco I asked around at my LQS. They recommended the Sewline fabric pencil. You can get both dark and white leads for it. It worked great until I lost it. :p Oh, well. Basically, it's just a mechanical pencil with marking leads. It was a bit pricy (about $15), though the clerk mentioned that she thought you could just buy the lead refills and put them in a mechanical pencil of the right size. I compromised by buying one, and switching the leads in it, lol.