[Therion] Under and over (maps)

Just come back from a day of gathering more data. I have set my maps up by area, then putting those areas into maps of cave. The new data has expanded one cave so that it is over another cave, my problem is that the same cave is under the other cave at a different point. Now it seems to me that the order of the maps is controlling the order of the layers on the pdf. So is the only way to fix this on the pdf to split the map (cave) up. The problem with this is if you colour by map (cave in my case) the cave would come out in 2 colours. Hope I have missed something Andrew