How to synchronize your computer
Synchronize in StepMania 3.9
There's a preference in StepMania 3.9 and newer called GlobalOffsetSeconds. You can adjust this by editing StepMania.ini.
Synchronize in StepMania 4.0
In StepMania 4.0, you can edit this value in-game using the AutoSync Machine feature (Shift+F6) or by using "Calibrate Sync" in Options.
In StepMania 4.0, there's a preference "VisualDelaySeconds". You can use that to specify the latency of your display and StepMania compensates only the visuals.