You don't. At least, not currently. That's one of the major drawbacks of the existing editor; there's no way to group layers.
My recommendation would be, if possible, to create the decal in a vector-based program and import it via the GT.com website. That way it can be resized easily. If you're sticking to in-game shapes, you'll want to make them the right size (and in the right place) for final placement.