You are looking at the difference between external and internal forces. The external force is the applied force (sometimes called a boundary force). Because of the application of an external force you will generate internal forces. This is because everything must satisfy Newtons law F=ma. So if you make "fictitious cuts" as they are sometimes called in solid mechanics at any position along the material and sum forces on that piece, the forces must sum up correctly. If the material is static that means the external forces sum to zero, likewise if you study the sum of forces on any element of the material the forces must sum to zero as well. On the other hand if there is a net external force on material it will accelerate. For the same reason the sum of forces on any element must equal to the (elemental mass)(acceleration). That is the basic idea...