It said to place 38kHz on one pin and 500 Hz on another and place the IR light "between" them.
It was not me but Udo Klein that said this.
It is simple, you have your emitter and resistor in series. You connect one end to one pin and the other end to the other pin. Then the emitter only lights up when one pin (the one connected to the anode) is high and the other is low. So when the low frequency pin is in the right state the LED flashes on an off at the rate of the high frequency pin. When the low frequency pin is in the wrong state the whole thing is off no matter what the other pin does. Hence the light pulses at the low frequency, but when it is on it is really being turned rapidly on and off.
If you have one pin producing a rapid change (38KHz) with the tone command (will tone actually produce ultrasonic sound?) then get one of the PWM pins. Change the PWM frequency to 500 Hz (or just try it as it is because some pins default to around this value) and wire up the IR emitter (and resistor) between those pins. Note the resistor needs to be such that the current is limited to below 40mA. If this does not give you enough range then arrange a transistor to switch them, possibly in an H-bridge configuration.