You can set the HW as the river bank and the TW as the storage area. Water flow over the structure will depend on the WSE in the river and SA, and the weir elevations for your LS. Your hydrograph will show positive flows from the river into the SA and negative flows once the river WSE enables the storage area to drain.
You could also set an outlet culvert for the SA to river flow. Your DS invert will be higher than the US invert. TW conditions will still control, but you can set the flap gates to only allow one-way flow.