It's interesting you say that, does that not mean you need to enroll both keys on every site you use them on?
This makes having one in a safe location somewhere kind of tricky, as it has to be accessible when you're signing up. so for example if you're travelling/working from another site, you won't have your "safe" key to hand.
Also you need to remember to do the enroll twice for every service, forget one, and you're back to trying to see if there's a fallback procedure.
I'm very surprised when people voice this concern. These keys cost a mere $20 or so. There's no limit to how many website you can set them up with. So $40 or even $60 is all you need to invest in.