I have never done scallops. But the principle is evenly spaced rounded areas, going into a rounded corner. When the quilters I know make scallops, they leave the border whole and quilt it first, then cut out the scallops. If you have a great long armer, they will quilt & mark the scallops for you to cut it out. If you are doing it yourself, then why not take a piece of freezer paper or wax paper or saran wrap and place it over the top of your border, then mark up the scallops using the pattern you have adjusted for the extra length. Once you get it like you want it, transfer markings to your fabric. I would use some that will come out or can be erased and then proceed to the quilting. I would mark the marked pieces with which side I was on when I did it. You might need to do it again if you lose the marks.
If you are making one of those self birthing scalloped borders, then the instructions will tell you whether to add them before or after the quilting and they can be FMQ separately. I have a Bali Wedding Star I am working on right now with scalloped edges. I am really thinking that I will birth the edges, hand sew that on the back and then decide if I really need any binding. The self birthing produces a completely finished edge, but it is only a single layer of fabric, not a double layer like binding is. Decisions, decisions. Always with quilting.