Jose,
The article you linked to is for a 9 volt source using the Super Cap. notice that the device is designed to supply about 1ma. If you read the sidebar, you will see that the referenced Super Cap can only supply 6 amps max at 2 volts.
The Super Caps, shown in the digikey catalog all have fairly high ESR, some as much as 30 ohms. A value of that magnitude would severely limit the current delivered to your motors.
Are you using any type of controller that would interface to spikes or other relays? If so, you could usually connect a relay to switch the caps between a motor and charge circuit, controlled by the robot controller. You might want to monitor the voltage across the cap and then switch to the internal battery when the cap voltage falls to a particular level. When that occurs just switch the motors to the other power source. Some of the caps on this page might be more of what you are looking for.
http://www.digikey.com/scripts/DkSea...sus.dll?Filter Values of 100,000 mfd at 6.3 volts for about $7 each. You can parallel these caps as I said before for larger values. They specify an ESR of 0.01 ohms, about the same as our competition batteries.