Right click on the amino acid residue you wish to modify and choose Edit/Attach Modifier.
Click on the molecular editor icon and use the tools in the molecular editor to sketch the modification you want.
In the molecule editor right click on the atom which will be the attachment point and select "Attachment Point". An asterisk will be placed on that atom.
Close the editor and then click OK in the "Covalently attach a chemical modifier" dialog box (see image above).