Atom map visibility should be turned on in View settings dialog to display the atom map numbers.
Unlike atom indices, map numbers remain constant during editing the molecule.
You can add map number to every single atom manually via the Atom properties dialog.
Open the Basic Tab in the dialog, and activate Map field by clicking the Padlock icon next to the input field. Type the number, then click OK.
You can change the number in this menu anytime.
To remove atom map numbers from atoms, you can delete the Map value in Atom properties dialog by closing the Padlock next to the input field.
Select the smart Reaction tool from the Tools toolbar, then press the left mouse button on the atom you would like to map, and drag to the other atom, which receives the same map number. (Golden brown feedback helps the process.) After releasing the mouse button, the atom map number appears on the lower-right corner of the selected atoms.
When there is no map number on any of the atoms, both of the atoms get the smallest number which is not present on the canvas.
In some cases, you need to map atoms with the same number as what another atom has.
Select the smart Reaction tool from the Tools toolbar, then press the left mouse button on the atom you would like to map, and drag to the other atom, which receives the same map number. As soon as the second atom gets a golden-brown feedback, release the mouse button.
The same happens when you drag from an atom which has no map number to another one which has one. Both of the atoms will get the same map number as what the latter one had.
Dragging from an atom which already has an atom map number to another atom with an atom map number, the latter atom will get the same number as what the former atom has.
Dragging from an atom with an atom map number to another atom with the same number results that both of the map numbers will be deleted from the canvas.
There is another option to assign map numbers to the corresponding atoms in a reaction.
Click the Auto Map button. In this case, every atom in the reaction will get an atom map number automatically. Please note that the Auto-map function only works for structures which are in the same reaction. (In other words: there should be only one reaction (one arrow) on the canvas where every molecule would be a reactant or a product of it.)