I have never done a panto other than messing around for a short spell on a practice piece. So far all I have done is freehand from the front of the machine and I quilt the borders as I go. Pantos are really intended for E2E quilting it would take a lot of futzing around to use a panto in the border as you describe, plus the added problems of causing wavey border like Kathy described. I have never run into this as I have never quilted the interior and then the borders, I am always quilting from one end to the other, changing my design depending on where I am in the quilt. If you are dead set on doing the panto design in the border perpendicular to what is in the body of the quilt, I would either make a photo copy of the panto on 8 1/2 by 14 legal size paper or actually cut a length off of the panto and place it on your table exactly how you want to quilt it. So you would need to measure out the part of your panto going the full width of the quilt and then carefully place the panto section intended for going the length of the quilt in the borders on either edge. This way you can follow your panto in the two different directions as you advance the quilt. However, unless you really know what you are doing and your measurements are impeccable, this method will create a certain amount of headache each time you advance the quilt. I can envision having problems lining up with each new section being quilted on the border edge. You will also have to get very creative when turning the corner. If I were you, I would try a free hand design in the border and your panto in the center and switch from front to back of machine depending on if you are in a border section or the center section.
I am sure there are LAers out here that have a lot more experience than me. There is probably a better alternative for you.