Firstly I am no expert machine quilter. But hees my 2c worth. If you go with the wavy lines (which I think would look really good) don't go over the applique (just up to the edge). As there are large blocks of colour, I would go for a matching colour thread for each part of the background (black on black etc.)...Ultimately, I think you will hit on something that will look great no matter which way you go.
Lovely design and great work....Please can we see it when it's finished?