Melanie, did you sleep last night ? That little piece is great. As you will practice you will gain more experience.
If you clip the organza, don't be afraid. Organza is so sheer so after quilting the hole will not be noticed ( I know because a few times I clipped mine).
If you cut the outline thread and that piece of batting don't want to stay in its place, you can stitch it by hand (or use a little glue).