I would prefer the diagonal mounting method, I am not a fan of drilling holes in the roof.
If you put it on top find structural members to attach mounting hardware.
Try to use existing mounting points to minimize putting holes in the roof.
For the back if the ladder is already there put one end of the Kayak between the hand rails, front end next to the air conditioning unit. From there you should be able to follow the stuctual member toward the right side for the final mounting hardware. Use those foam blocks that are shaped like the Kayak to support the Kayak.
Weather cock anything you disturb and any new mounting hardware. Inspect it regularly your through holes, and any place the Kayak or foam touches the roof.
Keep it clean any movement will act like sand paper.
Check this site, this boat is in my future.
http://www.orukayak.com/