Flood it till the water passes through. After that don't keep watering it. No reason to keep watering once its already reached the bottom. Its ok that the top floods as you fill. You could just water more slowly to prevent such flooding. But essentially what people are trying to say here is not to poor soo much water that it remains puddled up.
Also let the soil dry out before watering again. I think rule of thumb is like 5 days for 5 gallon bucket, but its best to just test it yourself by lifting it to see if its dry.