Mode toggle: click the toggle at the top of the settings panel to switch between Build mode (which lets you add electron domains around a central atom) and Pre-made mode which lets you select from a range of common examples.
Clicking and dragging in the empty space on the model box will rotate the model.
Clicking and dragging on any atom will drag it, allowing you to see how any other atoms respond.
Click the "Show bond angles" toggle to display bond angles (rounded to the nearest 0.5 degrees).
Click the "Show geometry" toggle to show the electron domain geometry and molecular geometry.
Click the "Show faces" toggle to show the 3D shape formed by the molecule.
Build mode
Click on the buttons for "single bond", "double bond", "triple bond" and "lone pair" to add each object.
Click on the red cross buttons to remove one of those objects.
You can add up to six objects around the central atom.
Pre-made mode
Select from the drop-down menu to view a molecule of your choice.
Click button to add, click cross to remove.
Pre-populates bonds and lone pairs for common molecules.
Adjust the relative strength of lone pair repulsion