I used the factory bars on my old Durango, also. My Toyota Highlander didn't come with crossbars, so I bought a pair of Thule bars.
To those, I added a pair of Hully rollers at the rear and a shaped block of wood at the front. The rollers make loading the PA14 a snap and also provide good support right under the scupper holes. The shaped block fits inside the drive hole and completely prevents any movement fore/aft and side/side. I use two ratchet straps midships and two bow lines to tow eyes in my front bumper.
It's a very secure system. Pictures:
