I like the Fons & Porter pump chalk pencil/pen in white for dark fabrics. I still mark lightly because the quilt needs to be washed to remove the chalk. I also like the blue pens that the mark erases with water on light fabrics. If it is staight quilting lines I use painter's tape as a quilting guide. I use the Frixion pens for small projects but not on quilts. Be aware that using them on dark fabrics can sometimes leave a light bleach? line.
If it's machine quilting, some people like the Golden thread paper that you stitch through. Some use tissue paper to stitch through. You can also mark the design on Glad Press & Seal that smooth that over the quilt square to quilt through. All of the paper/plastic have to be gently removed after the design is stitched. A lot of people use free motion quilting like Leah Day does on her website and the designs are not marked at all. There are as many ways and preferences as their are quilters. You will need to try several to find what works for you. ALWAYS try new methods on scraps before marking your quilt.