For example, If I want to: 

• Set apodization type as Gaussian, use the enumeration ZOSAPI.SystemData.ZemaxApodizationType.Gaussian.

• Set Apodization factor as 1

• Untick Fast Semi-Diameters

• Tick Adjust Index Data To Environment

The following code can be used: 

TheSystemData.Aperture.ApodizationType = ZOSAPI.SystemData.ZemaxApodizationType.Gaussian;
TheSystemData.Aperture.ApodizationFactor = 1;
TheSystemData.Aperture.FastSemiDiameters = false;
TheSystemData.Environment.AdjustIndexToEnvironment = true;

If I want to:

• Set Coating File as COATING.DAT

• Set Scatter Profile as SCATTER_PROFILE.DAT

• Set ABg Data File as ABG_DATA.DAT

• Reload above data files

• Add Title and Notes

The following code can be used: 

TheSystem.SystemData.Files.CoatingFile = 'COATING.DAT';
TheSystem.SystemData.Files.ScatterProfile = 'SCATTER_PROFILE.DAT';
TheSystem.SystemData.Files. .ABgDataFile = 'ABG_DATA.DAT';
TheSystem.SystemData.Files.ReloadFiles();
TheSystem.SystemData.TitleNotes.Title = 'Add here the title';
TheSystem.SystemData.TitleNotes.Notes = 'Add here the notes';