The basic idea behind BROOD is that you have a lead molecule and would like to generate analogs with somewhat different properties by changing a portion of the molecules. Normally, you will load the lead molecule into the GUI and select and edit the fragment you would like to replace. The GUI will also allow you to edit the chemical description of the query as well as define required motifs (constraints).
BROOD will search the database of fragments for fragments with similar shape, chemistry and electrostatics to your query fragment, replace them in your query molecule and generate a hitlist of analog molecules.
If you are just getting started with BROOD, we highly recommend you use the graphical interface. Even if you prefer to use the command line, walking through the graphical interface one time will give you a good overview of the workflow involved in running BROOD.