Stuff your down jacket down at the bottom of your bag, or wherever you are cold, and it will add extra warmth for you.
In addition to the tip above, where you but your Nalgene with boiled water in it, in your bag.  If you are feeling cold, and not feeling like your sleeping bag is providing you with enough warmth throughout the night, then you can add additional warmth by using your down jacket.  Stuff your down jacket down at the bottom of your bag, or wherever you are cold, and it will add extra warmth for you.