I picked up a 12" granite tile from the do it yourself place, had it checked for flatness by a machinist, and use it for all of my flattening. On my water stones, I just start rubbing a soaked stone, and its own grit flattens it. For coarse stones, I use some wet/dry paper.
The tile was $2.50, and the machinist charged me $0.00 to set it in a gizmo that had 0.00001" accuracy.