Yeah it’s not an easy molding to cut because the support structure it will rest on is not present…so…
I built a jig that fits exactly like the bar top and placed it under the arm rail to be sure it is in the same position as it will be on the actual bar top.
This will allow you to make the cuts in the proper orientation.
Since each type of arm rail is a little different, you’ll have to fab up your own jig based on what you’ve already built.
See: http://www.rockler.com/tech/RTD10000345AA.pdf
for more information on the available Rockler profiles.