If you want to set the extruder temperature in your Start G-code, you need to define it as {material_print_temperature, <extruder#>}. So, to set the print temperature for extuder #1 the code would be:
M104 S{material_print_temperature, 0} T0 ;Set extruder 1 to print temperature
M109 S{material_print_temperature, 0} T0 ;Stabilize extruder 1 print temperature
For extruder #2:
M104 S{material_print_temperature, 1} T1 ;Set extruder 2 to print temperature
M109 S{material_print_temperature, 1} T1 ;Stabilize extruder 2 print temperature