Tales of the Black Freighter was a "comic within a comic" in the original Watchmen graphic novel. In the book, a boy hangs out at a news stand reading this comic and talking to the stand's owner; all while the world is pretty much falling apart in the background.
That part is going to be left out of the Watchmen movie, but the DVD (when it comes out) will incorporate this animated version into the movie in the same way it was in the original book. But if you can't wait for that, the standalone DVD version of the anime will be released March 6 -- two weeks before the movie is in theatres. You can see the trailer below: