As with all things quilting it depends. How do you plan quilting it, by hand or machine? Have you picked out a quilting motif or are you going to echo the peicing? Is your quilting design a stencil, a template, a freehand motif or is it something you found in a printed media that you want to trace or duplicate?
I have marked the top before sandwiching and I have marked as I progressed. If you have templates, stencils or a freehand design you can easily mark as you progress. If it is something you want to trace you will have to mark the quilt before sandwiching.
Marking tools is another whole ball o' wax. I like using tools that will stand no chance of leaving a mark so I like to use chalk and Fons and Porter mechanical pencil with the ceramic lead. Down side is these all rub off easily so I must mark as I go. Additionally the Fons and Porter is a white lead so only shows on dark fabric. Chalk comes in different colors but I have had some difficulty removing blue chalk. Some use slivers of soap.
I have the water soluble pens but have not yet tried them. Again I plan on using those as I go and bought them for marking light colors.
I have entirely marked to full size bed quilts before quilting. On both of them it was a very light background where I had fancy motifs. I starched the finished top quite heavily then lightly marked with a plain old #2 pencil. The lead marks tended to stay on the starch so when I washed all marking lines washed out. But I was lucky, I have read about some that weren't so fortunate. There are also graphite pencils made especially for marking quilts. Just recently bought two, have yet to break them out and use them. For straight lines or 1/4" away from seams I use tape and do not mark.