How to power a Arduino Yun with a 6V battery?
Your best option is to get a separate 5V regulator (Linear or SMPS will work) to power the board from your battery. Digikey, Mouser or many other component distributors supply power regulators. A linear regulator would probably be the easiest to use. Generally there's an input pin, an output pin and a ground. You put the positive battery terminal on the input, the output pin to Vin and ground to ground on the Yun board and to the negative terminal of the battery. The regulator should be a 5V regulator obviously.
If this is somehow too costly, or you're under strict time constraints, you could probably get away with putting 2 high current diodes in series with the battery to Vin. This would drop approximately 1.4 volts from your battery voltage and hopefully get you in the range of 5 to 5.5 volts. 5.5 is the maximum rated voltage for your Atmega chip on there. Keep in mind this is a hack and should be done with caution. I do not recommend this method unless you're willing to potentially fry your board.