Jon,
I was on a FTC team for 4 years. What I have learned about the motors, is that when you see the "Magical Smoke", it is actually a resistor inside of the motor, and can be fixed by opening up the motor and replacing the resistor.
These motors are extremely susceptible to burning out when they are over driven. Take care not to use two motors on the same gear set, use the "big" gears with the "little" gears in a high torque situation, or to drive the motors under high torque for a long period of time (running into a wall, and keeping the wheels moving).
Our team just used some wire to hook up the motor directly to the battery (just be careful not to touch + and - together) to test them. It will not hurt the motors in any way.
Once you see smoke, the resistor inside has already been destroyed, and the motor is no longer going to operate like new. It may not be what you want to hear, but you are better off only using the "smoked" motors for testing components, and replacing the "smoked" motors on your competition robot.