I'm attempting to create subbasins for the deranged Aral Sea basin, which contains the major rivers Amu Darya and Syr Darya. I'm using a custom SRTM-GDEM blended DEM (90m postings in Albers Equal Area). When I prescreen sinks, if I set a low threshold for drainage area I get 1 million or more sink polygons. If I set a high threshold it misses the Aral Sea and Small Aral Sea (which are really all I need to leave as sinks as these are the end points for the Amu Darya and Syr Darya) because the area around the seas is very flat with many sinks each having a drainage area (it would be much preferable if Sink Prescreen allowed selection by sink area rather than drainage area).
So, I want to use a shapefile I have for the Aral Sea and Small Aral Sea as the only sinks, but the Create Sink Structures routine will not accept the shapefile (it wants HydroIDs assigned to the polygons?)
How to proceed?