So far Fassbender and Giger have confirmed that firstly ther is "a definite connecting vein" to the alien universe and Giger has also confirmed that prometheus does take part in the same universe as the Alien series. Then the bleeding cool leak went further to claim the alien aliens will be in it, but we may not recognise them, at least,not at first before going on to claim that prometheus does indeed take part in the same universe as alien. Now Scott has claimed that it is NOT a prequel and would say no more. EDIT - and now Fassbender joins the queue claiming it is NOT a prequel to Alien but confirms that it is definitely connected to the world of alien and that it doesn't ignore Alien, that the fans will recognize things in it.
This very recent info all points to the idea that Promethues may not be a prequel but probably will contain the aliens and the jockeys - therefore it will take part in the same universe for sure. It MAY be set before Alien, but probably won't end with the jockey travelling off to LV-426 or anything like that, or PERHAPS it will be set some other time, maybe even after alien, or at the same time? who knows? and is it really important? as long as it's set in the same universe and involves the Giger Alien species in it then I'm a happy man.