There's some controversy on the subject of watering by dunking. I personally don't do it, I water from the top only, pouring slowly to ensure that all of the soil is thoroughly wet and let it run through for a while. I am of the opinion that this allows needed air to get to the roots, while dunking causes the air to float out the top in the form of bubbles. Dunking will also cause any bark in the mix to float up and can move around the roots and cause an unanchored tree to tip over.
http://www.bonsai4me.com/Basics/Basics_Watering.html