Evidence for the emergence of twisted flux tubes into the solar atmosphere has, so far, come from indirect signatures. In this work, we investigate directly the topological input of twisted flux tube emergence by studying helicity and winding fluxes. In magnetohydrodynamic simulations with domains spanning from the top of the convection zone to the lower corona, we simulate the emergence of twisted flux tubes with a range of different initial field strengths. One important feature of this work is the inclusion of a convectively unstable layer beneath the photosphere. We find approximately self-similar behaviour in the helicity input for the different field strengths considered. As the tubes rise and reach the photosphere, there is a strong input of negative helicity since we consider left-handed twisted tubes. This phase is then followed by a reduction of the negative input and, for low initial field strengths, a net positive helicity input. This phase corresponds to the growing influence of convection on the field and the development of serpentine field structures during emergence. The winding flux can be used to detect when the twisted cores of the tubes reach the photosphere but this signature does not exhibit self-similar behaviour across the range of initial field strengths. In short, the helicity and winding fluxes can provide much information about how a magnetic field emerges that is not directly available from other sources, such as magnetograms.