This has been discussed so many times on the forum.
- You can deactivate sceneries installed using the add-on.xml method, from the Option->Add-ons menu
- Right now, the UI of the sim doesn't allow rearranging layers, even if the system internally supports it. We asked LM if they are planning to add this feature and, possibly, if enough users will ask for it, it might be added with an update. Or, it's possible someone might develop an utility to do that.