Click on the black triangle on the lower right corner of the Rectangle Selection combobutton to see the options of Selection.
Rectangle selection : Provides easy selection when the fragments can be drawn around with a rectangle. Hold the mouse button down while selecting; release the mouse when you are ready.
Freehand Selection : Push down the mouse button and move the mouse pointer around the fragment you would like to select then release the mouse button.
To select an atom , bond or group, click or select it (with active Rectangle Selection or Freehand Selection tool).
To select a structure you can double-click on one atom or a bond of it in Selection ( Rectangle or Freehand) mode.
One atom , or bond :
After selection (double click or selection by tool), move the molecule by dragging one of its atom. (See details here.)