I usually appliqué first but I have also made a few wallhangings where I quilted a grid & then machine appliquéd some flowers on. It makes the flower look a little like they've been stuffed, and also if you're doing 3D flowers you would need to attach them after quilting.

I made a Log cabin and my SIL loved it and I appliqued Canadian geese on it and then outline guilted the pieces but not thru the back layer. It came out great.