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If you are working at the ADF level, it's best to ask the DVT GeoMap related questions in the JDev/ADF forum. Even though based on an embedded mapViewer server (or the externally hosted maps.oracle.com service), the DVT GeoMap component provides its own interface and tooling which hides/limits what you can do with the underlying Mapviewer JS API.
You need create the THEMEs with mapbuilder, using tables with column geometry type for data geometry.
Later in ADF you can use dvt:mapColorTheme for show the THEMEs on map, is not necesary add THEME to BASE MAP on Mapbuilder.
Is very easy use THEME (based on table with geometry data) for show in map on demand.
May be next week I public a How To ... for more details.