Miata thermoswitch for auto trans
 

If replacing the FD thermoswitch with the Miata one in an auto tranny FD, is it just the one on the front of the filler neck? Is there another one behind the filler neck next to the alternator like on a manual trans?

The auto tranny actually has 3. A water thermoswitch and water level sensor for the motor and also a water thermoswitch for the tranny. The waterlevel sensonr and the auto tranny thermoswitch are on the front. The other is located behind.

So i would change the one in the back lower position to get the fans to come at lower temp, correct. What is the function of the switch for the tranny located in the front?

Yes, that is correct (the back ower position switch).