I would do the marked areas first and leave the fill in areas for last. When you have finished the marked areas, put the quilt on your design wall and look at it for a while. On most whole cloth quilts, a lot of the "negative" space is simply cross-hatched, but there are also areas where you could do stippling, feather motifs and echo quilting. Mark the areas where you want to do different techniques (if you don't want to mark the top, pin post-it notes on the top).