Temperature Controller List: This is where you'll have your extruders and heated bed listed. If you need to add an extruder/heated bed you would click the button for "Add Temperature Controller"
Temperature Identifier: The firmware identifier for this toolhead. Most printers use the notation for T0 for the Right Extruder and T1 for the Left Extruder. If you aren't 100% sure, you can open the Machine Control Panel and use the temperature identifier selector in that screen to find out what toolhead is which.
Temperature Controller Type: Sets whether your element is an extruder or heated bed. This makes a difference in the G-Code used to control it. For instance, the RepRap commands for an extruder are M104 and M109 whereas for a heated bed it's M140 and M190.
Relay Temperature between each: This will set how often to relay the temperature for USB prints.
Per-Layer Temperature Settings: Allows you to set temperature on a per layer basis. The temperatures that are set are read to the left. The adjustable numbers on the right do not effect your print, only when you click "Add Setpoint" are the temperature commands entered in.
Also, if printing with multiple processes, the layer # chosen is relative to the process. For instance, if this process applied from 5 mm to 10 mm on the model. The temperature for layer 1 would take place at the first layer after 5 mm.