Generally, you're just stitching the outline to mark your motif, and identify where you need to cut away the excess batting.
If for some design reason you needed to see a certain line within the trapunto, you can certainly stitch it now as well if you wanted. No harm done at all.
Just keep in mind that if you want to break up a design motif later, after the quilt top is sandwiched, the effect will be slightly different because it has the quilt batting in there as well.
You can easily make up a little sample just so you can see the different depths/poofs you get with different layers/types of batting.