My loading technique SHOULD have been to get one of those bars that slides out the side of the Yakima Bars, that would have made it easy. Or, I should have used your system with that suction cup thingy.
However, when you're taking two boats, you have two people. This was pretty simple. Strap the Ama's onto the main kayak. Get the second person to lift the stern of the boat while I lifted the front. Walk beside the car with the bow about equal to the front kayak rack (saddle). Lift the bow of the boat onto that rack, get the second person at the stern of the boat to walk forward, which will slide the boat forwards, when the weight balances out, you lift the back end up, and position it front to back by sliding it on the Mako Saddles. Many people don't know that the Yakima Mako Saddles have an optional custom fit felt pad that you can attach to the saddles. It's meant to protect the boat, but it's perfect for helping it slide front to back.
From there, you secure the straps which are already pre-loaded into the saddles, secure them. Slide the mast underneath the boat, between the saddles. The saddles will keep the mast from moving side to side, so a secure strapping down will keep it from moving front to back.
You can see that I put a couple extra straps securing the mast to the boat. That's just to prevent slapping, and is useful as another measure to keep the mast from moving front to back.
It's more complicated to describe than do, but it works perfectly. It's very secure. It's not the recommended way that Hobie says to carry the boat (right side up, instead of upside down), but I never had any problems with it. The Mako Saddles actually work as suspension to dull the sharp bumps and reduce the forces on the boat. I wouldn't drive a big tour with them, but I went several trips with it that were 4 and 6 hour drives.
(EDIT: The rear spoiler doesn't play into loading it as I load it from the side, and the straps are clear of it as the boat is long enough.
Also, the Mako Saddles work well because they HUG the boat all the way around, so when you tighten it, you're actually pushing it equally from every side, instead of strapping it DOWN onto a crossbar. I assume that Hobie recommends putting it upside down, at least in part, because the boat can be pulled down onto the cross bars in that position. The Mako Saddles can't dent the hull because of the way that they're secured to the boat. The largest pressure is against the sides of the boat, and not the hull.)