Just to clarify the terminology used to describe this scenario, are you referring to FSX / P3D run time rendering of:
* a CVX vector terrain-type polygon, either terrain mesh-clinging or flat with a 'continuous' altitude value used for all 3D-capable vertices placed at / near the assigned RWY altitude, made as a SHP2VEC-compiled "textured polygon" object ?
* a flat 3D model "Ground Polygon" (aka "GP" in ADE syntax) textured with a ground surface image, placed at / near the assigned RWY altitude, which is made as a SCASM-compiled or XtoMDL-compiled static 3D scenery object ?
Alternatively, are you instead trying to work with the object layer draw order in the ADE 2D work-space GUI ?
Not clear what you are asking. If you want to see the runway under the ground poly, why do you have the GP in the first place. If what you want to see is the runway under portion of the GP, there are a couple of ways to do it. The first is to create a "hollow" GP by making a poly in the shape of a "C" and then extend the ends until they just meet. Don't allow the end to overlap - which effectively accomplishes what Arno suggested. (Unfortunately, Arno, there's no way at the moment to "cut" a hole in an ADE-GP.) A second way, depending on exactly what you are trying to do, is to create a custom texture and use the alpha channel to create the "hole". It may also be helpful to know that there is a totally transparent stock GP texture named "gpTransparent".
When I have previously see the term "stock" used in ADE-related discussions I have consistently observed that a FS default or object such as an airport is being referred to, and that such entities would be found within a FS nested sub-folder..
Searching for "a totally transparent stock GP texture named "gpTransparent" ", only turned up this file / folder path:
And, truth be told, I have always thought it would be most appropriate for the term "default" to be used for any / all airports in their original format as provided by the original files within the nested sub-folder chains of a "default" installation of FS.
But since ADE might be viewed as having a primary function that involves de-compilation and copying of (mostly) airport source data that is then subject to further processing and modification to "Exclude and Replace" the "default" airport, I can see why Scruffyduck may have preferred use of 'stock' rather than 'default' ...to the intent- and extent- that "default" airports may be viewed as 'stock' "primitives" to be used for creating modified versions of the originals. ;-)