Hi from Punta Gorda!
Usually applique your blocks first, put them together, sandwich and then quilt. If you're appliqueing pieces on the border where where the border pieces meet, you would want to put the borders on and then applique those pieces that would go over the seams. Still, all before quilting....usually. But....it's your quilt. If you want to add some applique after quilting, that's entirely up to you.