These movies are an alternate retelling of the series. The first movie (1.0) follows very closely to the series, while the second movie starting to move away from the series and into new territory. At least that's what I've heard.

The first movie, 1.0: You Are (Not) Alone, and its various incarnations (the 1.01 extended cut, the 1.11 digital master cut, and the recent TV broadcast cut) covers the first 6 episodes of the TV series exactly. Some animation is taken from the TV series and touched up (moreso than for the Renewal/Platinum release of the TV series), other parts are modified, and still other parts are completely new (sometimes redone animation for existing events, sometimes completely new events). For example, the battle with the former third/current fourth angel is essentially the same as it appears in episode 2 of the TV series, while the battle with the former fifth/current sixth angel is essentially the same in terms of the things that happen, but is so much more completely awesome than its TV series counterpart. FUNimation is releasing the 1.01 cut later this year, and is releasing the 1.11 cut next year.

The second movie, 2.0: You Can (Not) Advance, covers up through the end of episode 19. Certain events from the TV series are revisited (and revised) amidst more new content. More new animation is added. A new character is added. Crazy things happen. The movie is as of yet unlicensed.