I print out an extra set of the four assembly layouts. i then glue them together with glue stick, cutting the margins to under a half inch.
Next I iron freezer paper to the front AND back of the entire block layout.
Cut them apart carefully on the lines and sort into color piles. The large multi-layer pieces are left intact and sorted into the pile for the outside color.
Fabric is cut with seam allowance around each paper piece.
I then use a mixture of liquid starch (1 unit) and water (2 units) to 'paint the seam allowance and iron them around the reinforced papers. (starch mixture is kept in my sprayer bottle and I use it for starching piecing and finished quilt tops.) I use two pins through each pattern and into my ironing surface to keep things in place. (a touch of washable glue stick now and then.)
Multiple layer pieces are first formed with the outside color, then the reinforced pattern is removed and re-cut for the next fabric.
Yes, this is a little more wasteful of the freezer paper, but It is quick and dead accurate as I am doing NO tracing, just cutting on the lines as they show through the freezer paper.
I use a light box, and Roxnne's Glue-Baste-it to attach my prepared applique pieces to the background.