I'm fairly certain that since River Song knows of an older Doctor, and because the Doctor will clearly be traveling in his own timeline which is apparently a big no-no, what's going to happen -- somehow -- is that the TARDIS is going to collide into itself. One will survive, one will not.
Since time is going to be rewritten, chances are the Doctor is going to take the TARDIS back into his own timeline (or someone else at the wheel may do it, which we know is a distinct possibility considering how smooth River was at piloting it as well as the whole 'does he know what you did' line) is going to wind up destroying his past self from the point of the collision up until the point of the collision. So, basically, most of this season. Though he's not going to have any idea that's going to happen, or if he does it's going to be some kind of suicide mission in order to save Amy and/or Rory.
That's my theory anyway. Seems to account for all the major points of the season thus far. Amelia seeing the TARDIS materialize in Amy's dream, why the Doctor found shrapnel from the TARDIS, the bishop's mysterious conversation with River, River's exceptional piloting skills, the cracks in time being caused by the TARDIS, why the supervillian aliens are mocking him about his impending death, etc.