I would stitch in the ditch (SID) first and then if you feel comfortable I would free motion around the applique to enhance it. SID is one of the first ways I attempted quilting on my machine.
BUT be sure you sandwich it without any wrinkles. I use the school glue method now and that has helped keep it from moving while quilting. Take you time when you sandwich...I thought is would be quick and easy when I first started, but taking time to be sure it is smooth is worth it.
You have done a great job...you must be so happy! I like that pattern too.