leave the PS3 turned on and change the settings to turn off the controller when the PS3 is turned off. You can turn the controller and the PS3 back on by pressing the PS3 emblem on the controller
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You use the charging cable to connect the PS3 to Controller and press the Playstation Emblem on the controller
When the PS3 is on use the charging cable to connect the controller to the PS3 and press the Playstation Emblem on the controller
Yes when your controller needs to be charged you can use the charging cable and still use the controller to play the game. Always make sure your system settings automatically turn off your controller when you turn off the PS3. Remember the PS3 will not charge the controller when it is off.
It does not take long for it to get enough of a charge for the red lights to work. Plus when the item is plugged in it has power and will work as a controller while it is charging.
There are no controller "slots" on the PS3. All of the controllers are wireless and are automatically mapped to which "slot" it is in depending on order of controller activation. To plug the controllers into a "slot" you could plug them into the USB ports, but this is not necessary unless you are charging your controller.