Operate is a re-skin of "Drive" which allows for the operation of any machinery in addition to vehicles. If it is a thing that is vaguely mechanical, and requires specialize knowledge, the "Operate" skill will determine how well you are able to make the thing work.
Overcome: The overcome action of Operate depends heavily on the nature of the machinery. In a Palace where operable Gundam-like mechas exist, "Operate" will work differently than in a Palace full of deadly mechanical traps. "Operate" may not work at all in a Palace of just fields and trees.
Create an Advantage: Again, this is very situational, but you can absolutely create advantages depending on what type of device you are operating.
Attack: Depending on the device, you may be able to attack with "Operate" (eg: set a bomb). However, with guns, "Operate" would not attack directly - "Aim" would be the attack skill.
Defend: Depending on the device, you can absolutely use this to avoid damage.