The preferences dialog allows you to manipulate various editor settings. Most of these are explained in the relevant sections. Those that are not, are detailed here.
To reset the preferences to the default (in case the current settings result in a problem that prevents you from accessing the preferences dialog), hold down the SHIFT key while starting SCI Companion.
If this is checked, the drawing tools in the pic editor will have grid lines extending out in each direction. This can be useful for lining up distant objects in a pic.
Use auto-suggest (as opposed to auto-complete) in edit boxes that support it (such as the Add As -> Synonym function of the script editor).
Open the last game when you start SCI Companion