I routed mine through the hole in the frame support behind the motor and above the transmission between the rear down tubes. You can't see it unless your looking for it. It only sticks out about 2 or 3 inches. It's out of the way and readily available to plug it in any time.
My bike (05) has a hole in the plate just ahead of the battery on the clutch side. I simply push the connector back in there, it's easy to pull out and can't be seen when stowed.
Mine is zipped and just sticks out a little in front part of left side cover, I use it to plug GPS in on longer trips. You could just take the cap off, run it arond the wire and put cap back on.