We prove that Manolescu and Woodward's Symplectic Instanton homology, and its twisted versions, are natural; and define maps associated to four dimensional cobordisms within this theory.This allows one to define representations of the mapping class group, the fundamental group and the first cohomology group with Z2 coefficients of a 3-manifold. We also provide a geometric interpretation of the maps appearing in the long exact sequence for symplectic instanton homology, together with vanishing criterions.