I don't have a headcanon for when they ended up, since we didn't see it and I think my actual headcanon is that we'll find out for sure later (because the Doctor lies, River lies, and we already know that facts of the universe don't actually mean they really happened).

But if they are back that far in time, I think they help found UNIT. And one day, maybe they're retired, maybe they're just busy, they hear some rumors about the newest scientific advisor. And they look at each other, and they're old and grey like the Doctor never wanted to see, and so they go, knowing he won't ever recognize him. And he's older too, but younger, and Amy wants to hug him but knows how psychic aliens work, so instead she settles for hugging Rory and keeping a weather eye on the advisor's assistant, and supplying them all with plenty of explosives.

Rory warns her about the daffodils, though.