As others have said...primarily depends on what marker you are using as well as how you are quilting. I've done both. I hand quilt. I find that marking as I go in sections - depending on the design - is easier as the marks don't fade/rub off as quick. For an allover design, however, I've marked the entire top before sandwiching. I use chalk in various colors depending on the fabrics in the quilt and/or #2 pencil.