Oh you have so many choices. I do kids name quilts with applique. I put the applique on just the front and batting. I use different colors for each animal for both bobbin and top thread, otherwise you'll get a peak of the bobbin color, even if tension is good. Once I load the color up I do everything on the quilt that needs that color.
If you are going to use one bobbin color grey is good for many colors. Then when I add the backing I do additional quilting on all three layers so that the quilting lines meet the batting specification.
You are braver than I am. I always use a print background as this hides many quilting mistakes and you don't have to worry about the back so much. Have fun and good luck.