The three-second rule means that it should take you three seconds to reach the point where the vehicle in front of you was when you started counting.
This is how you do it:
Pick a clear reference point, such as a verge marker or the shadow of a bridge above the road. When the vehicle in front of you passes the reference point, you start counting: "1001", "1002", "1003". If you reach the reference point yourself before you have counted to "1003" you are driving too close to the vehicle in front of you.
If you are driving a larger vehicle or towing a trailer, or if conditions are anything but ideal you need to increase your following distance even more.