Sounds like you're doing some dual extruder printing! What machine are you using?
Most firmwares will actually accept the T0/T1 parameters in-line with the M104 or M140 commands. So for example, to set the T0 extruder temperature it might look like "M104 S225 T0". Using an explicit T0/T1 by itself can actually cause some firmwares to run a toolchange command moving the axes and positioning the new head and the previous printing location (which can be BAD in some cases). So I would probably recommend using the in-line commands if your firmware supports it.
Thankfully the software has a really great and customizable firmware configuration for things like this. Go to Tools > Firmware Configuration and click on the FFF tab. You should see the command that is being used for "set extruder temperature" and "set bed temperature". Right now it probably says "M104 S$" and "M140 S$". Just change those to "M104 S$ T#" and "M140 S$ T#". The $ and # characters will be replaced by the setpoint temperature and the heater index.
Just be sure to verify those in-line commands work with your firmware first