I just installed a roof rack onto the bed of my tacoma. I'm not sure whether I should carry the boat upside down on the deck or let it sit flat on the underside of the hull. I tried it upside down age couldn't really find much flat deck space.
IMO, your racks are too close together. I have an older Tacoma with a square tow hitch receiver. I bought an "extend-a-truck" L-shaped and T-bar, attached my yakima cradles to it and put a yakima bar over the cab with cradles. To load, I wheel the AI to the tailgate, lift the bow up and place it on the raised tailgate (with a carpet or life jacket over it to protect the hull), walk around and lift the stern while pushing it foreward to the front cradles, then swing the stern into the rear cradles. I would never load an AI upright unless there were cradles under it to the hull doesn't deform.