I prefer the Frixion markers (they have a medium fine point) for marking my quilt designs.
I don't usually mark the whole design - only if I haven't used the design before and I'm trying it out. Usually, I just mark "landmarks," like the circle in a feather wreath and maybe the outside and inside limits for the feathers.
This was the way that I planned my most recent finish.
The markers last a long time if you keep them in ziplock bags when you're not working with them.
Edited to add: I always wash my quilts with several color catchers after I make them - they get softer and all the starch and manufacturing crap comes out of the fabric in a good wash.
I don't want to make a quilt for someone and give it to them "pristine," only to have a seam come apart or a patch to bleed into the nearby light fabric.
If a quilt looks better flatter, rather than the crinkly appearance after laundering, then I just iron it to bring back the "new fabric" look.