When you are setting up your flight in Free Flight mode, go to area #3 Current Weather and click on the "Change" button. The next menu will give you options for downloading realtime weather data but will also allow you to manually configure your temperature, windspeed, barometric pressure, etc. To set the variables yourself, click the circle next to "User-Defined Weather" and then the "Customize" tab below it; then, when the next screen opens, click on the "Advanced" tab.
Edit: you can also change the weather while in the sim by opening the menu bar (hold down the ALT key) and going to World ---> Weather.
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