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.
The reason why the mind is like this is because, in order to sleep, we must give ourselves into drowsiness. Those with untrained minds (if not everyone) thus plunge themselves into delusion. That's why in dreams, everything's all loopy and oftentimes you don't realize that you're dreaming. When you wake up, your mind is just emerging from that state.
I think what happens with most is that they get worked up over the drowsiness they experience when they wake up, so they assume their mind has gone down the rabbit hole. But it hasn't, unless you're getting worked up about the drowsiness! It's simply another experience of the aggregates.
So when I wake up, what I do is remember the conditioned nature of experience in terms of the aggregates, particularly the part which deals with contact and the sense-bases. Whatever you see is an eye-object accompanied by feeling, perception, and volition. The same applies to the other sense bases. This gets my mind back in the grove because our practice involves great use of the 6-sense bases, until you get to the formless states of samatha meditation. How could you investigate the elements without the sense bases? What is their to develop dispassion towards if it isn't the senses?
In your waking life, using the aggregates as your work station, investigate drowsiness so you can understand it more and not become worried because of it. There's the feeling in the body, the passion towards the feeling (a volitional formation which manifests as laziness and leads us to taking a nice, comfy rest on our bed... or desk)... just try to understand it more.
I hope this solves your problem.
This is my personal opinion. Process of fabrication goes on which you are asleep. My rationalising ia as follows
Your mind is muddled since your sleepiness and perhaps the fabrication during the night. So when you do wake up start getting aware of your body part by part initially take large parts. Then do a little bit or breath meditation focussing more on the sensation on the spot (Philtrum / Columella). This will charge you up to overcome lethargy.
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This little plant of Dhamma requires service now. Protect it from the criticism of others by making a distinction between the theory, to which some might object, and the practice, which is acceptable to all. Don’t allow such criticism to stop your practice. Meditate one hour in the morning and one hour in the evening. This regular, daily practice is essential. At first it may seem a heavy burden to devote two hours a day to meditation, but you will soon find that much time will be saved that was wasted in the past. Firstly, you will need less time for sleep. Secondly, you will be able to complete your work more quickly, because your capacity for work will increase. When a problem arises you will remain balanced, and will be able immediately to find the correct solution. As you become established in the technique, you will find that having meditated in the morning, you are full of energy throughout the day, without any agitation.
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When you go to bed at night, for five minutes be aware of sensations anywhere in the body before you fall asleep. Next morning, as soon as you wake up, again observe sensations within for five minutes. These few minutes of meditation immediately before falling asleep and after waking up will prove very helpful.
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Daily meditation of two hours and yearly retreats of ten days are only the minimum necessary to maintain the practice. If you have more free time, you should use it for meditation. You may do short courses of a week, or a few days, even one day. In such short courses, devote the first one third of your time to the practice of Anapana, and the rest to Vipassana.
Source: The Discourse Summaries by S.N.Goenka
We don't actually know in full detail why we sleep yet, be we do know that it seems to be because our mind needs to recuperate from being used all day. Even dolphins, who you'd think cannot really sleep because they'd drown have found a way: their left and right hemispheres sleep alternately. Given that nature is willing to jump through such loops, I think it's safe to say that sleep is pretty necessary.
In order to be able to recuperate, it makes sense that it must be to some extent turned off. People aren't machines however; there's no single switch that can be flicked to activate us. So it takes a while. You aren't bothered by sankharas, you're just not really quite there yet when you wake up.
I've also read recently that some biologists noted that in mice extra fluid enters their little brains, apparently to sort of wash them. I think this must surely interfere with normal awareness, otherwise the extra fluid would be there all the time. Maybe draining it away takes time.
But whatever the case may be, what you're experiencing is perfectly natural and nothing to worry about. Maybe you could try starting to wake up earlier, but doing it more gently?
