Beyond Compare is highly configurable, and it sometimes can be hard to know where to go in the program to change a specific setting. Here's where to look:
General user preferences are set in the Options dialog. Pick Tools > Options to open it. From here you can set startup options, control confirmation messages, and customize display colors and fonts.
Most of the options that define the scope and rules of a comparison can be found in the Session Settings dialog. Each session type has its own session settings dialog. Pick Session > Session Settings to open the dialog, or simply click the Rules toolbar button.
Session settings are stored with your saved sessions.
Specific file types can be configured in the File Formats dialog. Pick Tools > File Formats to open it.
Specific remote services can be configured in the Profiles dialog. Pick Tools > Profiles to open it.
Source Control Integration
Specific source control associations can be configured in the Source Control Integration dialog. Pick Tools > Source Control Integration to open it.