Do you plan on quilting through the applique or echoing around it?
How do you plan on adhering the applique to the fabric?
If you use a fusible to adhere the applique to the fabric you will still need to stitch the edges of the applique to make it permanent (fusible is not permanent), and typically this is done before quilting. If you machine stitched the applique down, then when hand quilting did an echo stitch around the applique - that would work. But I wouldn't recommend trying to hand quilt through the applique that has been fused down.
Another way to adhere the applique to the fabric though is to use an elmers glue stick to stick the fabric down, then machine stitch the edges down. The glue stick will hold for quite a while (days) as long as you don't handle it too much - and DO NOT iron it. It's a bit easier than quilting through fusible, but still a bit more difficult because of the extra layer of fabric.