I had some initial trouble getting STO working. First, Twinview meant that the game was trying to stretch across two displays to my full 3840x1080, and second, the audio stuttered annoyingly in the background. I solved these issues easily:
To solve the stuttering audio, I went to the Control Panel for my STO bottle (XP) and set the audio driver to Alsa, changing it from Full acceleration to emulated.
While in the control panel, I went to the graphics tab and set STO to run in a desktop of 1440x900 (which would fit).
I ran the game it ignored the resolution setting, but at least was on one screen. I then set the graphics properties in game to run in a window maximised, applied the settings, and exited the game (and steam). I then went went back in the control panel and unchecked the emulated desktop setting. STO now runs as well (IF NOT BETTER!) than it did in Windows 7.