Yes, I've done that with fiber fill. I like it better with yarn, but lack the patience for all the times you have to feed the yarn though. I really love doing true trapunto better than the faux trapunto that has become so popular recently. You can get puffier results & don't need to quilt the living daylights out of the background to create the illusion that one extra layer of batting makes it really puffy. They are both beautiful options, but my clear preference is to actually stuff the applique.
So excited to see your final result! Hope you post pictures!!!