That is a very good question, and a full description of van der Waals forces between molecules is actually an active research topic in theoretical chemistry. However, to a good approximation, for most molecules you can assume that the attractive part of van der Waals force (known more formally as "dispersion" interaction) from each atom is independent of its neighbours, so you can calculate the force between two molecules as the sum of forces over pairs of atoms. For some molecules, especially those with delocalised electrons, there are more complex "many-body" dispersion effects, but these require some advanced quantum mechanics to work out.
For atoms in the same molecule, we generally ignore van der Waals forces, as they are negigible compared to bonding interactions (covalent, ionic, etc). For neutral molecules, especially those with large numbers of electrons, then van der Waals forces can contribute significantly to intermolecular bonding.