What do you guys that carry canoes do with the antenna? Does it create problems or does it fit inside the hull nicely?
First of all, I am not aware of any other member that transports canoes. I'd like to see some pics if someone else does.
Second, I generally leave the antenna in place when transporting my canoes. The antenna does not stick up all that far and there is a ton of clearance before interfering with the hull.
That being said, depending on the size and configuration of your canoe, you may run into a situation where the antenna interferes with the seat and/or any yokes or crossmembers.
If you plan to leave the antenna in place, be extremely mindful of it.
The antenna will break off if you slam a gunwale into it, leaving the stud broken off in the base. If you break it off, good luck extracting that broken stud. There was a post a while back where a member broke the antenna while washing his wife's sonic, or something along those lines. IRRC, the shop quoted him in the ballpark of $300 to fix it. Not sure whatever came of that.
The obvious thing to do is to un-screw the antenna before loading/unloading your canoe. It takes all of about 10 seconds and is nice insurance against a costly PITA repair. Once the canoe is loaded on the roof, you can screw it back on if you really need that extra reception. Personally, I don't think the antenna does much of a damn thing, and I get poor reception even with it on. I much prefer to play music from the USB anyway.
The best solution would be to buy a shark fin when they become available again and not have to worry about it ever again.
Now, time for some questions of my own:
What rack do you have?
Where do you plan to attach your tie-down lines for the bow/stern?
What size canoe do you have?
Finally, I know a thing or two about hauling canoes on the Sonic. Feel free to ask me any questions that you might have.
Good luck and share a picture when you get around to it.