Company Prefs are on the second tab of the Company card on the System toolbar. These settings affect all Users (unless they override with their own User Prefs). All Connect settings for APIs are found here except Web-Server and Web-API settings that are per-user and found on Employee card.
This Solution decribes this feature. (6493)
Prefs like Auto Zoom affect all Users that are set to "System Setting" so you can change all at once (to use larger Zoomed windows). In their User Prefs they can change from System Setting to control their own settings (unless User Settings Prefs is set to Hide). Also, you can view and change User Settings in the Employees Search.