Here's what I think is happening:
The villains respond to the cracks by devising a plan to trap the Doctor in the Pandorica before the TARDIS can explode. The trap kicks off when the Atraxi have a random encounter with the Doctor when he visits young Amy. The alliance takes advantage of his quick hop in the TARDIS to bump his arrival until after they're able to whip up a fake town complete with a fake grown Amy, who accompanies the Doctor in his travels with the ultimate goal of bringing him to the Pandorica.
This set up explains why the Doctor finds the town strange, the odd details like modern cell phones but outdated name tags, why Amy doesn't know of the Daleks, how the alliance knows how Rory is killed, why Amy has a made up job, why she tries to force a relationship with the Doctor etc.
However (and there's always a however), the alliance is actually the victim of a double bluff by a heretofore unknown third party who is conniving to trap the Doctor in the Pandorica
before he can stop the TARDIS from exploding. This is the voice in the TARDIS, the one person who stands to benefit from destroying the universe of matter ... Omega.
The Doctor will use the power of the anti matter universe to set things right (remember how it works in The Three Doctors) and restore the universe of matter with the help of some careful nips back in time to talk to the young Amy and console the fake Amy in the Byzantium, where presumably he needs her help to stave off the most aggressive of the cracks we've seen to date. Finally, at the end of the episode he'll hop forward to the
real Leadworth and find the
real Amy, who will travel in the TARDIS as his companion for season two.
But I'm probably completely wrong!