My current theory is:
At the end of The Pandorica Opens everything in all Universes was erased except for Earth, so at that time Earth would have been the Doctor's home planet (as it was the only planet).
When the Doctor flies the Pandorica into the Tardis he then flies back across his own timeline (naughty) to put things in place so that he can be brought back from being erased from existance. In doing this we notice some discrepencies (like the jacket where we now know the two doctors existed simultaneously.
At the end of The Big Bang Amy manages to bring the Doctor back so we have the Doctor who never existed (except in last series skewed timeline) appear at Amy's wedding.
Closing the crack meant that the alternate timeline never happened, meaning that the Doctor never got captured in the Pandorica, then got erased from existance, so Amy and Rory's wedding was part of the normal timeline where the Doctor existed and had met Amy as a child but presumably nothing else.
Now where it get's complex. If the alternate timeline doctor did not appear at Amy's wedding then the alternate Timeline would have to have happened and everything wiped out. In technical terms this is a Predestination or Self Fulfilling Paradox. The Alternate timeline Doctor has to be at Amy's wedding because he was there (same explanation for how he escaped the Pandorica - How did he get out, because he was out already even though he was locked in - He was there because he was there - Check Wikipedia).
If the above is true then at the moment of Amy's wedding there are actually two Doctors. The real Timeline one and the Alternate Timeline one, one of these knows Amy as a child, the other has travelled with Amy and could believe that Earth is his Home Planet.