How to wake up properly after a nights sleep? My mind tends to be more unbalanced after waking up than before going to bed. I try to observe breath and sensations but the mind is pretty muddled. This raises the question if the mind is making sankharas in deep sleep too? How is that possible when I don't have a choice in the matter? 

What are the best practices after waking up?
One simple way to setup your mind in the morning is to re-take the refuge vow and/or the five precepts. Or, if you are a Mahayana practitioner, recite the Bodhisattva vow. 

Here is another consideration though: as one of my teachers said, "the morning begins in the evening". Your morning mind is continuation of the tendencies you have setup in the evening. So if you go to bed with a clear mind and pure heart of simplicity, chances are, you will wake up clean and bright. The state of mind during the day matters too. If we argue, or get obsessed, or blame ourselves during the day, these thoughts and moods tend to come back during the night.

In the evening, there is a number of ways to prepare your mind for a good night. In my opinion, meditation should be done earlier in the evening, before the sunset. After sunset, having a silent walk helps. What I personally do after that, is read a Buddhist book in bed. This only works if your practice is going well though, otherwise you may get a sense of guilt when comparing the high ideals with your actual state.