I use pool noodles for my yaks and also load them top side down. They just seem to fit better. As far as tie-downs, it is recommended to tie on bow and stern lines as well as the normal straps around the yaks at the x-bars. I never use a tie down on the stern, but almost always use a tiedown on the bows. The only time I do not tie down the bow is if I am traveling a short distance at a slower speed.
There is a great way to tie down the bow. Raise the hood of your vehicle and at each front corner under the hood near the seam you will notice a bolt. This is a fender bolt that can easily be removed. Take a piece of webbing strap and double it making a loop several inches in length. 3 or 4 should be plenty. Make a hole through the 2 ends of the loop (or install a grommet). Pass the fender bolt that was removed through the holes in the strap and then replace and tighten bolt. You now have a loop of webbing at each corner that you can pass a line through to tie down the bow of the yak. When not in use, the loops can be tucked under the hood out of sight, out of mind until needed again. Keeps from crawling on the ground looking for a tie down point under the front of the vehicle. If you look closer at Oak Orchards website, you will see these loops for sale, but you can easily make them much cheaper. Good luck.
The pic below shows my setup and the bow tie downs can barely be seen.
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