Highlighting Valence Errors when checked, highlights atoms having wrong valences with red underline. This option can be set separately for MarvinSketch and MarvinView.
Automatic Lone Pair Calculation calculates lone pairs automatically. Make sure View > Misc > Lone Pairs is checked to see the result.
Validate S-groups At Creation disables the S-group types in the drop-down list which would not yield a chemically correct structure. For more information on S-groups click here.
Carbon Labels options determine the condition of displaying C labels on carbon atoms.
Ligand Orders options determine in which cases to display the ligand order information for an R-group.