Thank you for the replies!
Okay, I will applique onto the borders before I attach (that's what I thought would make sense, glad to hear y'all affirm it!).
I do the quilting myself, by machine. I use my Flynn Frame which makes it fairly easy to maneuver. What I was thinking was to quilt now sans border/applique, then add both and add the final quilting, sort of like quilt as you go. But I'm thinking just waiting and doing all the quilting once the top is done would make sense...