Hi lordauriel,
The underwater transition is a switch between "on" and "off", so there is not a gradual transition, or ability to do a splitscreen type of effect (though this is something I'm working on for 3.0). What you may be able to do in order to reduce or eliminate the obvious problem shown in your screenshot is to adjust at what height the transition kicks in. You can do this on the Suimono_Module object under 'general settings' by lwoering the 'underwater transition threshold' setting. This can be lowered to negative numbers if necessary. I recommend trying something between 0 and -0.15.
This isn't a perfect solution. Another possibility is to write a control script for your scene camera that keeps it lockd to a certain height above the water until it hits a certain underwater position, and then switching the lock to be underwater. This is a bit involved, but is a common way underwater transitions are handled in games to avoid showing artifacts like this.
As mentioned this is hopefully something that I can completely eliminate in 3.0 version. In my prototypes I've redone the water so it renders in screenspace and in that case there is much more control over how the transitions can be accomplished. I don't have a projected release date for 3.0 yet, but it is something I am working diligently on.
