Canoe Tie-Down Help

I have a 2010 VW Jetta SW TDI and I just purchased an aluminum 11'x40" canoe. While this is a short canoe, it's quite wide and I'm have a really difficult time figuring out the best way to tie it down to the Jetta. Currently, I'm using foam canoe blocks and ropes right on the bare roof (eek) that strap down to the roof rack. I had finagled my dealer to throw in cross bars when I purchased the car, but the canoe is actually wider than the crossbars (it's also wider than the roof rack at it's widest point) so it seems less stable on the crossbars than on the bare roof with blocks. However, I'm noticing that as I tie the canoe down it's causing the roof to pop in a bit so I'm obviously doing damage to the car, not to mention I've caused some awesome scratches to both the roof and the roof rack (though I'm using some rolled up carpet now to guide the canoe on the roof so that's cutting down on the scratches). Any advice on a better way to strap a very wide flat-bottomed canoe to the Sportwagen?

Also, here's my totally n00b question. So far I've just been using the cross-ties, but I purchased some Thule ties for the front and back of the canoe. However, when I went to use them today I found that VW only included one tow eye so I can only use it in the front or back. Do you guys usually buy a second tow eye or is there another place under the car that can be used for tie-downs? I did check the manual, and stuck my head under the car, but found nothing.

Thanks for the help, I really appreciate it!
-Rebecca