We’ve strapped our 17’ Big Chief on the stock rack on our ‘08 using those dense foam blocks and they lift it a good bit, should give you the clearance you need. Another cheap option is pool noodles, but beware noodles are made from difference types of foam, some are more spongy, some are more rigid and once they deform they don’t recover their shape, try to get the spongy ones. The spongy ones are also better for doing noodle beer bongs, in case you are throwing an adult pool party or have a fun group of people with you at the campsite.

Buy a Reese Canoe/Kayak loader from Amazon for about $30. It attaches to your trailer hitch. It has an upright bar attached to a T-Bar that swivels. You simply load one end of boart onto the t-bar. Secure this end to t-bar with bungee cord provided. You then lift the end of boat that is resting on the ground, and walk it to front of roof, while the boat pivots on the t-bar.
This simple, inexpensive solution has allowed me to load my Hobie Kayak by myself. It also provides a third support point for you boat, the other 2 supports being your roof rack.
My Hobie weighs 85lbs and presents no issues for rooftopping.
I use a small trailer when I fish locally, but going out of town, the Hobie goes on the roof.
https://www.amazon.com/Reese-Towpowe...s%2C153&sr=8-1

Attached Images

 

Here's my tandem kayak setup (so similar dimensions to a full canoe). OEM rails/crossbars + Yakima Sweet Roll kayak rack.



Definitely clears the spoiler when mounted, but it has scraped a few times when rolling it up onto the feet (we ended up putting down a strip of clear PPF film along the spoiler to help). As for tiedowns, I just use the OEM towhook up front and the hitch in back (not pictured).