Low Battery
When an active controller gets a low battery, the PS3 will display a message in the upper-left corner of your screen alerting you to charge the controller. Additionally, the single light that indicates the player order will begin to flash. This light will continue to flash until you either turn off the controller or plug it in to charge. You can check a controller's battery level at any time by pressing the "PS" button. The rechargeable batteries in the PS3 controller have a limited lifespan; over time and several charges, the battery may hold less of a charge.
Charging
When you plug your controller into a power source -- be it via USB cable into your console or a charging station -- the four port indicator lights will blink. These lights will continue to blink the entire time you charge your controller, unless the controller is in use. If you use the controller while it is charging, only the player indicator will be lit up, without flashing. You can only charge the controller via USB cable while the PS3 is on.
Connecting
While connecting to the console and assigning a player number, the four port indicators on the controller will blink for a couple of seconds until the controller assigns the number. If you have not used the controller with your console before, or if you're using your controller at a friend's house, you will need to connect the controller via USB to pair the devices; this will clear the current pairing in the controller. You will need to do this every time you use the controller with a new console. If your PS3 controller flashes and does not connect, you may need to reset the controller.
Resetting Your Controller
You may need to reset the controller if your controller has a full charge and will not connect to your system even after being properly paired. On the back of the body of the controller is the information sticker. Just above the upper-right corner of the sticker is a small hole -- this is where the reset button is hidden. Using a paper clip or some other small thin object, push the button inside this hole. Once you've reset the controller, press the PS button again.