If you like to keep the top down and under the cover, check out a product at California Car Covers called "The Duster". It covers from the wiper blades back to the trunk very nicely, and doesn't touch the paint anywhere.

 

Update on the cover!! Yesterday, I had top down all day so I put cover on. I totally forgot is and used my remote top. Not a good idea!! I think I got to it before any damage as its working fine now but I was expecting a blown line or damaged pump. Whew!!

 

I always try to put the tonneau on the down headliner. On some real short trips I didn't bother. The couple of times I didn't bother to put on the tonneau cover and I always kicked myself for it later.
I can see where the headliner seams can start coming apart from the harsh thrashing about in the wind.

 

Join the club. I don't have the remote thing but once having the top down for several days (with the tonneau of course) decided to put the top up. So I pushed the button and heard the motor for a second and then nothing. I feared the pump blew out again and then looked around to discover I had forgotten to remove the tonneau. No harm no foul since once removing it the top worked fine. I guess there is some failsafe that will turn off the pump if it feels too much resistance.

Doug

 

Yeah, now that my interior is completely balck, it looks great without the cover!