I was always told to work from the background forward, i.e. applique the flower to the background, then the centre to the flower. This would make it easier to keep layers flat. The only time I would do it the other way around was if, for instance, the flower were a large one, and I wanted to cut down on layers of fabric. Then I would sew on the centre of the flower, and cut away some of the flower from behind the centre. Then applique the flower to the background, and I could then cut away some of the background from behind the flower. With this method, you have to be careful making the first cut, and take into account that you must leave a quarter inch seam allowance.