I appliqued my first quilt onto the borders and had issues at the corners.....
In the second, I left the outside of the pieces (elongated hexies) "open" -- that is I didn't fold them over (or I unfolded them) so I would have a straight line to be able to sew the seam via the machine. I tended to like the 2nd better because I got much straighter/flatter seams. I haven't FMQ'd it yet, but it is next in the queue.