There is at least 1 extra AF1. Not only used as a decoy but in the event one of the other plane has a mechanical issue...
I know I watched the President departing some location recently on TV and the coverage showed him board the plane. As it taxiied away, a second AF1 followed right behind.
As far as Marine 1’s, I had all three of them fly over my head on 9/12/09 when I was in DC for the March on Washington. It was late afternoon as as we were making our way back to our tour bus, all 3 Marine 1 copters flew over (I was by the Washington Monument) before 2 peeled off leaving the one carrying Obama to land. He had left that morning as the crowd was forming on Pennsylvania Ave, for a trip to Minnesota to get out of town. But he first circled the city to see the massive throng of Tea Partiers gathered for the day.
I was there! If I had know he was flying over, I would have flipped him the bird. In a polite, Christian way.
Hope he counted all 1 to 2 million of us.
By convention, whatever aircraft POTUS is in, is either AF1 or Marine 1. The others, the spares, go by different call sign.