Startup options
When Beyond Compare starts up, it normally shows the Home view. To have the program automatically start up with the same sessions that were open the last time you used Beyond Compare, specify the same workspace name in the Load workspace and On Exit, save workspace as edits. In the Session menu, you can also use the Save Workspace As and Load Workspace commands for further control.
When you start Beyond Compare with a pair of files specified, the program can display a dialog with a comparison summary, rather than taking the time to display the entire side-by-side comparison. To preface a file comparison with the Quick Compare dialog:
1.Mark the When starting with file comparison, show quick compare dialog checkbox.
2.Pick Binary quick compare to perform a byte-by-byte comparison, or Rules-based quick compare to use the file format settings appropriate for the specified files.
3.Mark the Open view automatically if files are different checkbox if you want the dialog to only appear when the files match.
To run Clipboard Compare on Windows startup 
Mark the Run Clipboard Compare on Windows startup checkbox. The Clipboard Compare is a small system tray application that can be used to compare recent Windows clipboard entries.
To add Beyond Compare to Explorer's right-click menu
Mark the Include Beyond Compare in Explorer context menu checkbox.
Pick any of the optional commands listed in the table and pick Main menu or Submenu to include it in the context menu. Enable Compare Using to add a submenu that lists specific views, such as the Table Compare view and the Hex Compare view. This allows you to override the view that would normally be selected via the file formats list. Enable Merge to add 3-way merge support to the context menu. Enable Sync to support synchronizing folders from Explorer. Enable Edit to support editing a single file from Explorer. Enable Compare to Registry to support comparing a registry file to the live registry.