Notice how the parameter values in the second configuration are automatically calculated by ZEMAX, according to the temperature assigned to that configuration. 

Update the 3D layout to show both configurations. The top-half of plot in the layout below is the configuration at higher temperature.




You can clearly see the effect of the thermal expansion on the location of the second window. You can also notice  in the multi-configuration editor the change in window thickness and semi-diameter values.

Now, let's say that only surfaces 3 and 4 in the second configuration are at 1000 degrees. You need to insert another TEMP operand so that those surfaces are at different temperature than operands under the first TEMP operand.

Insert a second TEMP operand after all the operands that belongs to surfaces 1 and 2 and set the values to 20 for configuration 1 and 1000 for configuration 2. 



Notice how the thickness of surface 3 is larger than surface 2 in the second configuration.