For this type of airfoil, the 50% chord is the thickest part of the airfoil (as opposed to the quarter chord for most). The best way to line up your line is to eyeball the end of the canard and look for the thickest portion---make a mark. Then measure this mark from the back edge of the canard (not the elevator---but the aft edge in front of the elevator. With an accurate measurement, you can lay out a couple of measuring marks on the "right" and "left" canard. From here, you can snap a chalk line. Use the template to draw the vg marks (I used a small magic marker---can't see the mark with the vg on top---even though the vg is clear. Use silicone to attach them.
My connection in Iraq is not letting me see my homepage---but if you look on my page, you will see the layout of vgs---this will give you an idea of the layout that you need. I had spare vgs left over when I was done.