Using the selection interface, you select the ligand then click the ligand design icon to enter ligand design mode.

In ligand design mode, the ligand is initially in selection colors, so the entire molecule is in shades of blue. This makes it difficult to pick out nitrogen, oxygen is kind of purple, and good luck telling sulfur from fluorine. (I'm assuming "Ligand Specific" and "Cartoon Ligand" view options.)

When atoms are selected, a selection halo appears around each selected atom, and the rest of the molecule reverts to normal coloring.

When atom selections are cleared, the molecule reverts to blue selected.

Having the ligand appear in normal deselected colors while in Ligand Design mode would make it easier to see what's going on.