Magnetic flux structures in single crystals of the layered spin triplet superconductor Sr$_{2}$RuO$_{4}$ are studied by scanning micro SQUID Force microscopy. Vortex chains appear as the applied field is tilted along the in-plane direction of the superconductor. The vortex chains align along the direction of the in-plane component of the applied magnetic field. The decoration of in-plane vortices by crossing Abrikosov vortices is observed: two vortex orientations are apparent simultaneously, one along the layers and the other perpendicular to the layers. The crossing vortices appear preferentially on the in-plane vortices.