Hi, John
If you have added lots of layers to one plug-in and upon receiving one GetMap request for this plug-in and by default we will render all the layers included in one plug-in depend the sequence you added to MapConfiguration, and that means the latter added layer will be added to top of the returned tile image. So if you want to control the order of layers precisely, and I suggest that you let the layer whose order is indeterminate is only included in one plugin.
As for every one request, you can request more than one plugin using the LAYERS parameter, so you can control the order on the client-side with ease, and don’t forget to add STYLES parameter for everyone plugin.
Please let us know if you still have any questions.
Thanks,
Khalil