Oh YAY NEVERMIND I FOUND OUT HOW AND OMG NEW ORDER TILESET CHANGES EVERYTHING ABOUT HOW TILES ARE HANDLED BEWARE!!!
*edit*
I have created a layering system its quite simple , anyone ever see the Newworld backtile system? well I have scripted something similar it was realy realy easy
I will post a version of it l8r tonight after work
However it only does transparencies for foreground objects however I will add more to it tonight