MarvinSketch provides enhanced stereochemical representations.

Using the Atom menu or Atom popup menu, you can set the configuration of each chirality center in a molecule.

The absolute configuration of a chiral molecule can also be defined by using Structure Menu.

To see R/S labels in the structure and the geometric (E/Z) isomerism set the Stereo options in View Menu.

You can find more information on the scientific background of stereochemistry here.