Duration/Removal of the effect
There is no way to remove the efffect. It takes anywhere from a few seconds to a minute and a half for the automaton to cool off and no longer be overloaded. Duration of the effect is believed to be related to the length of time the automaton has been out as well as the number and element of maneuvers up at the time of overloading.
Example: Overloading from using one Light Maneuver right after summoning your automaton will not last as long as an overload effect from spamming Fire Maneuvers after having your automaton out and having been using maneuvers for a longer period of time.
How Overload is induced and how to avoid it
Overload occurs when a Puppetmaster uses a maneuver(s) too soon after summoning the automaton, using maneuvers too soon after having zoned with the automaton out, or using maneuvers too frequently, especially multiple maneuvers of the same element. Using a maneuver immediately after overload wears can result in overloading again.
To avoid overloading it is best to use maneuvers of varying elements which help to cancel each other out. Water Maneuver helps to reduce fatigue from Fire Maneuver, etc. Timing of when you use your maneuvers can also help greatly. If you have three maneuvers up already, wait until the oldest one wears off before replacing it. Wearing Puppetry Dastanas while executing a maneuver will also reduce the risk of overloading.
The Puppetmaster's 2-hour special, Overdrive, temporarily prevents overload from occuring. It does not, however, prevent the build-up of elemental fatigue. For example, if several Fire Maneuvers are spammed during overdrive, you would not become overloaded, but if a fire maneuver were used immediately after overdrive wore off, then you would likely overload.