Question
2 stations come on at the same time even when the system is set on manual to run one station.

Answer
There may be a problem with the wiring connections for the valves.  Each valve should have two wires, one that is unique to a numbered terminal on the controller, and a second wire that is common to all valves and connected to the "common" terminal on the controller.  The connections should be sound.  Check out the link below for a great irrigation tutorial.

http://www.irrigationtutorials.com/instal08.htm