I'd say to make the one with the higher invert your secondary. Each outlet (primary & secondary) will have two components, the orifice and the pipe. Make sure the orifice are routed through the pipes they are in.
Can't model storage from pipe and CB interconnecting two ponds. I have a parking lot with two subcatchments. A CB at the bottom of each basin. First pond flows to second via a pipe (culvert). Downstream CB has a vertical orifice restrictor plate at outlet invert. When I add the pipe and...