Hi Shay,
First off, I wanted to let you know that trying to read a thermocouple with a USB-6009 is not the most accurate system in the world.
The USB-6009 has 14-bit resolution with a minimum range of +/- 1 volt. This gives a voltage resolution of 122 microvolts. The estimate of the response of different thermocouple types can be seen below.
Common thermocouple types have the following response:
K type: 41 microVolts per degree Celsius
J type: 56 microVolts per degree Celsius
T type: 52 microVolts per degree CelsiusEssentially that means that if you are using a K Type thermocouple then you are only going to notice a change of temperature for every 3 Degrees C (~5.5 Degrees F). This might work for your application, but just keep in mind that you have pretty poor resolution when trying to read a thermocouple with a USB-6009.
Other than that, for the switch you can't source much amperage from the USB device, but other than that, just do a digital output and it should work fine.