Remember that it is easier to retain your body heat than to lose it and try to get it back.  After hiking and setting up camp and you are done sweating change into your warm, dry sleeping clothes and PUT ON A HAT while you are around camp.  Put on enough warm clothes to be comfortable but not sweating again.  Eat a lot of fats for your supper, they will digest slowly and warm you at 3 in the morning.  Once you have the correct gear then it is a matter of regulating your food intake and paying attention to warmth retention. 

During the night squeeze your toes or fingers to create circulation.  The chemical hand warmers are great for an unexpected dip but you should rely on you basic equipment (bag and pad) for the majority of your trips. 

And remember anything draped over your puffy sleeping bag will have the effect of lowering the effectiveness of that insulation (unless it is a lighter puffy thing like maybe a down jacket).  Lots of experience talking here from a chronically cold person.