Directly as in Alien would begin where prometheus left off. I've seen the movie now and it is NOT a direct prequel to Alien. It's more like Phantom of the menace for star wars where it starts a new story and a couple films later on it leads directly to original series. Of course prometheus is directly related to alien, but it's not the direct prequel to alien. The biggest questions all alien fans had from the original films were who were the space jockeys, what were the xenomorph eggs doing on their ship, where were they flying to and what the hell were the xenomorphs? Too many these questions are left unanswered and they've created a bunch of new questions.
movie is fucking awesome tho.