Fluid flow through sub-micron domains has been an area of active research in recent years with immense scientific and technological interests. Such flows can show deviation in behavior from the theories of classical hydrodynamics thus opening up a new paradigm to exploit these unique effects in applications related to transport and detection. By performing extensive molecular dynamics (MD) simulations of fluid flow through a parallel plate nanochannel of non-uniform wetting characteristics, we bring out the coupled effect of surface wettability and applied body force on interfacial slip. Our results reveal distinctive slip-stick alteration which can be useful in designing channels with engineered effective slip. Moreover, in this study, we revisit a hybrid molecular-continuum multiscale model which can significantly reduce the computational cost of full scale MD simulations and further provide a framework to discern the flow behavior for a wide spectrum of length scales. The results obtained from this study may provide useful insights thus carrying immense implications towards designing of multifaceted nanoscale devices and futuristic smart surfaces.