You forgot to add "while heading for deeper water"!
My biggest objection to the thermal layer in the game is it's a solid flat plane which unrealistically works 100% every time - in real life the temperature and salinity changes to the layers can be mild - moderate - strong, they can make the detection anywhere from slightly more difficult to impossible depending on how sharp the temperature change is, instead of going from perfect sonar conditions to the Klingon cloaking device.
One thing to keep in mind for the game though - the temperature sensor is on the keel of the sub. When you get the message "passing thermal layer" (can be anywhere from 150 to 250 feet, although it's usually less than 200) you need to get the whole sub under the layer - at least 60 feet deeper than the message depth. Again it's a flat plane similar to the surface - if you submerge to 35 feet the top of the conning tower and periscope shears are sticking up above the surface and are visible to lookouts at close range. The thermal layer is programmed (oversimplified!) the same way, if the thermal layer is at 180 and you're at 215 feet, the top of the conning tower and periscope shears are "visible" to sonar since they're above the layer. At a keel depth of 240 feet the tops of the periscope shears are five feet below the layer, so "invisible" to sonar.
One tactic in shallow seas I've used, got a task force cruising along in 100 feet of water, but his course will take him over deeper water about 12 hours from now - so I parallel his course (10 to 15 thousand yards ahead) matching his speed until my fathometer indicates deeper water, then I submerge and wait for him to arrive.