If you can, place the watermarks on a layer and bring the layer to the front by moving it to the top of the Layers panel.
In the WatermarkPreferences there is a property called watermarkDrawInBack, that could be set to false (I think it is set to true by default).
Just try this (not tested):
app.documents.watermarkPreferences.watermarkDrawInBack = false;
If you mean the script DocumentWatermark.jsx from the Scripting Guide of the SDK, just change the line 23 of the code:
myDocument.watermarkPreferences.watermarkDrawInBack = false;
Thank Uwe, it works.