The arrow tool provides the easiest manual way to map corresponding reactant and product atoms.

Select the arrow tool, hold down the left mouse button on a reactant atom, and drag it to the corresponding product atom. The same map number is added to both atoms marking, that they represent the same atom on the two sides of the reaction scheme.

Similar tool "Manual Atom Map" can be added by customization.

There are also keyboard shortcuts for mapping. Type m8, for example, and click on an atom. Atom map 8 is assigned to that atom.

Marvin contains an automapper tool as well (available as Structure > Mapping > Map Atoms) assigning map numbers to all selected atoms of a reaction automatically.

Map numbers of the selected atoms can be removed by the Structure > Mapping > Unmap Atoms menu item, or by typing m0 for the selected atoms.