Vertical turbulent mixing in ocean boundary layers is critical for understanding the transport of environmentally and biogeochemically important tracers, especially in coastal regions where surface boundary layer (SBL) and bottom boundary layer (BBL) can overlap and merge. This merging boundary layer (MBL) regime poses a particular challenge for existing vertical mixing parameterizations in ocean general circulation models. In this study, we use idealized large-eddy simulations (LES) to investigate vertical tracer transport while the SBL and BBL overlap before they fully merge. We consider an SBL driven by aligned wind and waves and a BBL driven by a steady current that is either aligned with or opposite to the surface wind. Time evolution of buoyancy and passive tracers released from both boundaries is analyzed to diagnose how cross-boundary exchange develops, why the aligned and opposite configurations differ, and how Stokes drift modifies the middle-layer shear and stratification that control the tracer transport. While strong stratification exists between the SBL and BBL, tracers released from either boundary progressively enter the opposite boundary layer. A bulk transport efficiency is used to quantify this cross-layer exchange efficiency. The forcing orientation produces distinct transport pathways, which can be attributed to Eulerian shear production of turbulence kinetic energy and the interaction between turbulent momentum flux and velocity shear. We further use a spatial filter to separate small-scale turbulence from large-scale coherent flows. We find that time evolution of the bulk transport efficiency is better correlated with small-scale shear production, mostly due to changes in the momentum flux rather than the magnitude of shear. While Stokes drift decays rapidly with depth, it strengthens and reorganizes the momentum flux in the middle layer. These results are useful for future improvement of ocean vertical mixing parameterizations especially in the MBL regime.