Does anyone know how to change which polygon is on top when 2 polygons from the same dataset (continental shape files) overlap? Specifically, I am working in the Gulf of Mexico and have created a separate PlateID for the transitional crust, it needs to appear when it is still partially covered in places. When it appears it sits on top of the Yucatan, instead of underneath it so it can be fully revealed as the Yucatan rotates.
AFAIK you cannot control this - GPlates behaves the very same way as your standard (Arc/Q-)GIS. The only way to have full control about this is to split the data into separate layers. Or subdivide it into smaller polygons which appearance once they are no longer fully or partly covered by your overlying polygon.
Christian is right, you can only control the order of layers (files essentially).
Within a layer the order is currently hardwired sort by plate ID to ensure a consistent, stable rendering order when polygons overlap (eg, reconstructed rasters and filled polygons).