I've done several quilts on my Janome 6600. I have used the quilt rolls where a pattern is printed on rolls and you can stick it onto your fabric. And I have also traced patterns on Golden Threads paper and pinned it on. (It takes longer but you get good results). If you are using light fabric you can mark it with an air erase pen.
I start in the middle of the quilt and pin all around the center and work out from there - always working from the center to the outside. (I roll up both sides so I have room). I really don't pin the whole quilt at once as you always have to move the pins anyway. So I pin each section as I go. Make a sandwich of fabric and batting to practice first to get a speed that's good for you and once you get into a groove you should be all set.