I'm trying to figure this out better too. If you have smaller bottles, you can keep them in your shirt/parka/fleece. If they don't get cold when you make camp, I suppose you could throw them straight into your sleeping bag. You can also boil one of those bottles before tossing it into your bag to make for a nice warm night.

I figure that even if a bottle freezes, if you'll be hiking hard the next day, it'll warm up pretty quick under a shirt.

Still though, I don't have much experience in freezing temps. I'd like to know if those with more experience do things a different better way.