Magnetic fields extend from the solar interior through the atmosphere. The formation and evolution of active regions can be studied by measuring subsurface flows with local helioseismology. The emergence of magnetic flux from the solar convection zone is associated with acoustic perturbation signatures. In near-surface layers, the average dynamics can be determined for emerging regions. MHD simulations of the emergence of a twisted flux tube show how magnetic twist and free energy are transported from the interior into the corona and the dynamic signatures associated with such transport in the photospheric and sub-photospheric layers. The subsurface twisted flux tube does not emerge into the corona as a whole in emerging active regions. Shear flows at the polarity inversion line and coherent vortical motions in the subsurface flux tubes are the major means by which twist is transported into the corona, leading to the formation of sigmoid-shaped coronal magnetic fields capable of driving solar eruptions. The transport of twist can be followed from the interior by using the kinetic helicity of subsurface flows as a proxy of magnetic helicity; this quantity holds great promise for improving the understanding of eruptive phenomena. Waves are not only vital for studying the link between the solar interior and the surface but for linking the photosphere with the corona as well. Acoustic waves that propagate from the surface into the magnetically structured, dynamic atmosphere undergo mode conversion and refraction. These effects enable atmospheric seismology to determine the topography of magnetic canopies in the solar atmosphere. Inclined magnetic fields lower the cut-off frequency so that low frequency waves can leak into the outer atmosphere. Recent high resolution, high cadence observations of waves and oscillations in the solar atmosphere, have lead to a renewed interest in the potential role of waves as a heating mechanism. In light of their potential contribution to the heating of the solar atmosphere, some of the recent observations of waves and oscillations and ongoing modelling efforts are reviewed.