You can record Tone 1 and Tone 2 seperately and simultaneously on different tracks in your recording program as long as your program has the ability to record at least two simultaneous tracks. I would be surprised if yours did not. As you suggest, you should set up your X3 preset to use Tone 1 as your guitar tone and Tone 2 for your vocals. Use the X3 usb connection to your computer, and configure your recording software to use the X3 and its ASIO driver as your audio device.

Once you have armed your two tracks for recording in your recording program, select the Tone 1 and Tone 2 options for each track in the Record Input selection area associated with each track in your recording program.