Usage of physical book covers?

I got S&M Ecstasy in the mail just today, and I'm really happy with the purchase! It's beautiful. However, the color cover on it is actually a loose cover, with a different cover inside. It seems that the inner cover would be the one used while reading the book, as the outer cover would slip around and stuff while holding. So I was wondering, what do you guys do with the book covers? Do you store them elsewhere, and just keep the book on the shelf without the outer cover? Or do you keep it on and remove the cover to read? Or just deal with it?