"Have you seen the movie yet?" is most typical. "Have you already seen the movie?" suggests that you would be surprised is I said yes. "Have you seen the movie already?" is the same as number 2, but less common. The word "yet" goes at the end of a question, but the word "already" normally goes before the main verb. Putting "already" at the end of a question is OK, but it sounds much more emphatic. "Have you been reading 3 hours by now?" is a bit strange; I'm not sure I understand exactly what you mean. I would probably say "Have you already been reading for three hours?" Which implies that the asker would be somewhat surprised if I answered yes. Also, not that this last example is present perfect continuous, meaning the action was was started in the past and is still happening. Btw, I'm curious what your name "UnKraut" means.

the first two mean the same. The last one asks if the reader is now still reading and has started at least 3 hours previously.