The first thing I would want to think through is thread color. Are you going to go with a neutral, try to match the fabric in each block, or go with something striking/contrasty that calls attention to the quiliting?
My approach is to take a photo of the completed quilt top, print it out full page size, and then doodle some ideas for free motion quilting. I don't actually mark the quilt top -- I just go into it with some idea of what I'm going to do, and have at it.
RST