The file namelist.output.da (which contains the complete namelist settings) will be generated after a successful run of da_wrfvar.exe. The settings appearing in namelist.output.da, but not specified in your namelist.input, are the default values from $WRFDA_DIR/Registry/registry.var.
After successful completion, wrfvar_output (the WRFDA analysis file, i.e. the new initial condition for WRF) should appear in the working directory along with a number of diagnostic files. Text files containing various diagnostics will be explained in the WRFDA Diagnostics section.