In this case force F refers to the total external force, on the system (internal forces in the system are not included in F) and a refers to the acceleration of the whole system, i.e., acceleration of the centre of mass of the system.
In this case force F refers to the total external force, on the system (internal forces in the system are not included in F) and a refers to the acceleration of the whole system, i.e., acceleration of the centre of mass of the system.