ADE9X and Megascenery

I recently started playing around with ADE9X to modify a local airport. I also have Megascenery X Socal and noticed that it has the same airport identifier bgl file in it. This is the file I have used to do my changes as Megascenery has done most of the heavy lifting of changing the taxiway alinements and moving the signage and buildings to match the photo scenery. I have done some minor tweaking of a runway and some PAPI and VASI lighting and it looks really good. One thing I have noticed though is that Megascenery's bgl file contains only the items that Megascenery worked on, but does not contain any of the buildings, execpt the tower, and is missing one runway that are in the FSX bgl file though the buildings were obviously moved to fit the photoscenery. Since I would like to do some more tweaks I would like to know how the two bgl files relate to each other so that if I do something in one I won't end up messing up the other?