This section of the Preferences panel lets you determine what stations are automatically opened, what panels (if any) appear on launch, whether you want the Menu Extra installed, and if the application gets hidden immediately:
These options take effect on the next launch of the application - and they try to work together. For example, if you launch with Command Center or Multiple Station, the individual Thermos won’t be opened. If Menu Extra Only is selected, only the Primary Station is opened.