Add a methyl group to the methane

Go to the structures menu
Select the 'Methyl' structure from the 'Alkyl Chains' submenu

Notice that the button of the structure menu has turned black, which means that the structure-tool is in use.

Double-click on one of the hydrogen atoms

You will see that the hydrogen is replaced by a methyl group.

Note that:

• The methyl is orientated along the newly formed C-C bond and the new hydrogens point
  away from the existing ones.
• The double-clicked hydrogen is replaced by the carbon atom, since this atom is the 'replacing' atom.
  This atom is defined through having xyz-coordinates (0,0,0).
• The Structures button turned red, you are using the select-tool again.