You don't set anything. SH3Commander sets both the depth of the layer and the percentage of 'opacity' to the sensors randomly on it's own each time you start up. The settings are universal anywhere you are in the world and do not vary until you restart the game with SH3Commander.
You can't control it without making a permanent setting in a config file which IMHO is a little too predictable.
Even the SH3Commander thermal layer is rather unrealistic as in the Atlantic the themal layers are much deeper than in the Pacific and in most places far deeper than most of the WWII subs were capable of diving.
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