I do a combination. Usually I mark as I go using either white chalk or a sliver of soap for dark fabrics and the purple air eraseable pen for light fabrics. But, for some projects I use the blue water soluble marker to create the basic lines that I want to use to divide the quilt since I want those divisions to stay on the whole time I’m quilting. Any places where the blue lines cross dark and can’t be seen get ”joined” as I go using a sliver of soap or white chalk.
either way, I almost always mark after I baste.
Rob