Set them just like any other properties.
Create a map (typically <String, Object> ), add properties by name – including their namespace – with their values to the map.
Finally, use cmisobject.updateProperties( ) to add/update the properties on the object.
Or, when you create the object initially, just add them to the initial createDocument or createFolder method call.
Maybe I'm not understanding the question, because if you're creating objects, you probably know this already.
-AJ