You should always put the addon airport on top of any photoreal scenery.
However, a double centerline looks more like a double afcad, I don't know if Swiss Pro comes with any AFCAD, but they might usually come also with traffic package products.
You can use some of the available utilities for FSX to check for AFCAD files. For example, this one:
http://www.scruffyduckscenery.co.uk/index.htmlYou should have only 2 AFCAD BGLs for Geneva, the stock one, and the FSDT one. And of course, Geneva should always be on top of the layer list, which is were its installer will automatically put it anyway.