You only put back in, what you've used (like gasoline in a real car).
eg: Let's say you only ran the car for a few seconds and used up only 20mAh, and then charged that same battery. It will keep charging very low (0.01-0.30 amps or whatever) for hours, until the safety cutoff turns off the charger... very likely the timer safety first, before the capacity safety ..since you've only used 20mAh and there's no way it's going to pump in an extra 4500mAh (or whatever your battery's capacity is) into an already full battery. Hope that made sense.
When I start seeing my charger becoming low/slow on the amps (hovering between .01-.20), it usually means the battery is full and then I shut it off.