XBeach is configured using a collection of files that hold information on the bathymertry, boundary conditions, model settings, etcetera. All files are plain text files that should be in a single directory, the model run directory. Running the XBeach executable in this directory, will make XBeach use those files and save the model output in the very same directory.
Setting up a model implies creating these files in any way of your preference. Common tools that are used to setup an XBeach model are:
RFGrid and QuickIn
Matlab and the OpenEarth Matlab toolbox for XBeach
How these files should look like is described on the XBeach documentation website at:
This website also provides some basic tutorials and example model schematizations.