What is the proper way (order) to wake up in the morning, wash netilas yadaim, say the beracha of al netilas yadaim and asher yatzar etc…?
The common custom is as follows: After waking up, netilas yadaim is washed immediately — either by means of a bowl next to the bed (for those who do not walk 4 cubits before doing netilas yadaim), or by the sink. Because a person usually needs to be excused after waking up, the berachah is not made straight away (because: 1. it is improper to make a blessing when needing to be excused; 2. one aspect of netilas yadaim is as preparation for prayer, and one cannot pray before seeing to bodily needs). Rather, netilas yadaim is washed again after getting dressed and seeing to one’s bodily needs. After washing, before the hands are dried, the blessing of al netilas yadaim is made, and this blessing is followed by the two blessings of asher yatzar and elo-hai neshamah. If upon waking up one does not need to be excused, one should say the three blessing immediately following the netilas yadaim after waking up. One should then be careful to avoid touching covered parts of the body while getting dressed, because this would reqiured another netilas yadaim before prayer.
[This is the standard custom for those who follow the custom of Ashkenaz; some have the custom of reciting the blessing (al netilas yadaim) in shul, and some wash netilas yadaim only once.]
Sources: Shulchan Aruch (Orach Chaim 6); Mishnah Berurah (4:2-4).