It takes place exactly when we see it within the narrative - Amy's timeline is presented in a pretty linear fashion. What is confusing is why, at that point, Amy now remembers the '5:02' timeline just because the audience has now seen it. It suggests the possibility that the Doctor and River did alter the original timeline somehow when they negated the alternate reality.
1. 1996; Amelia Pond meets the Doctor at the age of 7. He promises to be back in five minutes.
2. 2008; Amy Pond meets the Doctor again and they have their encounter with Prisoner Zero and the Atraxi.
3. 2010; the Doctor returns and Amy joins him on his travels. Amy marries Rory on June 26th; the universe is rebooted and Amy and Rory conceive Melody/River aboard the TARDIS.
4. Amy and Rory enjoy a multi-legged honeymoon, visiting the honeymoon planet and taking a trip on the starliner.
5. Between "A Christmas Carol" and Series 6, Amy and Rory return to Earth, before being invited to watch the Doctor's apparent death. Pregnant Amy is captured by the Kovarian Chapter of the Silence and replaced with a Flesh avatar.
6. The Flesh Amy and Rory travel in the TARDIS from "The Impossible Astronaut" to "The Almost People". They witness the future Doctor appear to die at Lake Silencio, but cannot reveal the happening to 'their' Doctor. The real Amy later gives birth on Demon's Run, but the baby is taken by Kovarian.
7. Amy and Rory go back to Earth while the Doctor tries to track down Melody. Amy and Rory travel to 1938 with the Doctor and Mels, learning along the way that Mels is Melody/River.
8. Amy and Rory travel with the Doctor from "Night Terrors" to "The God Complex", before the Doctor 'saves' them by taking them home for good, buying them a house and a car and telling them to get on with their lives. Amy believes that this is the last time she'll ever see him, as she assumes that the Doctor will not visit them again before he meets his destiny at Lake Silencio.
9. Amy becomes a model, and the face of Petrichor. She experiences memories of the alternate timeline created when River refused to kill the Doctor at Silencio. River comes to her with news that the Doctor did not die at the Lake, and Amy is ecstatic to realise that she will probably see him again.
10. Two years pass for the Ponds before the Doctor turns up on their doorstep for Christmas dinner. For the Doctor, over two hundred years have passed.
11. Amy and Rory break up and almost divorce before reconciling. They travel in the TARDIS sporadically for a while before rejoining full-time.
12. The Weeping Angels send Rory and Amy back in time, and because 'time' says that their paths never cross with the Doctor's again, the Doctor has to abide by this, lest the temporal anomalies tear New York apart (as they're centred there - so even if the Doctor were to simply arrange to meet them in Singapore, New York would still burn; what matters is that the Doctor never seeing the Ponds again has become a fixed point in time, and geographical location has no bearing).
13. Amy and Rory live out the rest of their lives in 20th Century New York, eventually dying in their eighties. Amy became a children's author under her married name, Amelia Williams, penning Summer Falls (a favourite of Clara Oswald and containing a character called 'the Curator'...).