You can use the second switch, but you have to connect the switch a little bit different like the first.
For switching on you have to use the sw pin to ground with a button normally open. The Pin ON you have to connect with the PowercontrolPin of the arduino. This Pin must be configured, that it goes HIGH after turning on the Tonuino. If the PowercontrolPin goes to LOW from the StandbyTimer the Pololu will turn OFF. The slideswitch on the Pololu have to stay in the OFF position all times. If you turn On the Tonuino you have to press the ON Button for 3 to 5 seconds, till the PowercontrolPin of the Arduino is going HIGH. If you press the ON Button to short the Tonuino will not stay in the ON mode.