Are you supposed to say the bracha al netilas yadayim after doing negel vasser after waking up or going to the bathroom?
You are supposed to say the Berachah upon washing your hands in the morning. (Shulchan Aruch O"C 4:1)
It seems from the Shulchan Aruch (O"C 7:1-2) that you do not need to make a Berachah even if you find that you need to wash your hands after using the bathroom, because you are only required to wash then for cleanliness - in fact, you may not need to wash at all, depending on the condition of your hands afterwards. The GR"A (ibid., S"K 2) explains that this is because the sages enacted the law of washing upon rising because we are like a new creation, as well as before eating (although he doesn't explain this last point), but not for any other purpose.
However, I have heard that, according to some, you are supposed to say the Berachah after using the bathroom, depending on what you were doing in the bathroom, I have not seen a source for this idea.
I was taught that the "best" way is to wash negel vaser in bed without a bracha, then go to the bathroom, get dressed or at least be decent, wash again, say al netilas yadayim, say asher yotzar, and then say the rest of brochas. I used to do it a different way that involved only washing once, as I think a lot of people do. I don't remember when you say the bracha if done that way, but I think it is still at the end.