I think the voltage may be too low to run the l.e.d. at that current. Putting cells (batteries) in parallel doubles amperage, not voltage. I'm not saying to put both cells in series and run it directly, that would make the voltage too high. I think you need a boost circuit for one cell or a buck circuit or resistor for two cells to get the right voltage. L.e.d.s have a voltage range they operate in. Too much voltage fries the l.e.d., too little doesn't light it up. Within that operating range, voltage determines how much current it will use. At the low end, it will take less voltage and current and be dimmer. At the upper end, it will use the maximum amount of current and voltage the l.e.d. is rated for and be the brightest. Find out what voltage is required to run the l.e.d. at 3 amps and plan the circuitry accordingly.
