ChemDraw: Automatic Caption with Number for Molecules
There is no fully automatic method for creating labels. However, you can manually generate property labels, which are automatically placed and centred without disturbing any existing alignment, as follows.

Select the entire molecule, right-click the selected structure, then click Analysis, and then click one of the available options (Name, Chemical Formula, Exact Mass, Molecular Weight, m/z, or Elemental Analysis):



Use the Text tool (on the tool bar) to modify the text of the label (after your edit, you will receive the warning “This change to the text has caused auto-updating to be disabled.”): 



You can use the Text menu, the Style toolbar, or shortcut keys (e.g. CTRL+B) to change the text format (structure labels are usually written in bold). Repeat this procedure for all relevant structures: