The main window of BinNavi is your starting point whenever you are working with BinNavi. It gives you an overview of the content in your BinNavi database. Information about your disassembled files, your reverse engineering projects, and many other related things can be found here.
The graph windows are where you are doing code analysis. You can use them to read through flow graphs full of disassembled code and to debug your target file to get more information about its states.
To change global BinNavi settings you can use the Global Settings dialog.
To change the default settings of flow graphs and call graphs you can use the Graph Settings dialog.
This section contains information about using the integrated BinNavi debugger to debug target processes.