First off, take a look at this thread, it addresses some of your question- http://www.flightsim.com/vbfs/showth...uestion-(KEQY)
You exclude is technically called a switch and not a file. It can be added to any active scenery area, so you might try moving it to another scenery area that has lower priority than KRVD.
To get the layered effect you are looking for first create a grass apron, then place the macadam runway on top of it.
Afcad does not have the ability to create a flatten for your airport.
Some elements flatten terrain by default, including aprons and taxiways. Oddly enough runways will not flatten the terrain, but you can work around that by placing an apron under your runway.
But you will not flatten terrain between these different elements, leading to buttes and holes between them.
The proper way to do this is the way MS did it.
First you have to create a flatten file to prepare the area.
Then you need an airport background to mask the underlying landclass and eliminate autogen trees and buildings. Roads and powerlines are another story.
They are vector scenery and immune to common exclude methods, however they can be edited.
The tool you need for FS9 is SBuilder. It is the bulldozer that can do all of the prep work for your airfield.
Again, follow the link I posted, go to FSDelevoper and get SBuilder and spend some time with the tutorials.
Once you learn how to do this it really doesn't take long to do, though you can spend as much time as you want, to do these things.
Lastly, Afcad is past it's prime and you should give ADE a try.
WWOD---What Would Opa Do?
Farewell, my freind (sp)