Hmm, I am a very accomplished scenery designer, but what you are describing leaves me a little confused.
The airfield you are trying to make is not in X-plane, yet the runway is in the custom scenery?
I think your problem is beyond this basic Q+A site, why don´t you go to the more dedicated scenery building site at x-plane.org? I am sure people will help you there. Just some basic hints:
You can´t move the default X-Plane roads, but you can suppress them with an exclusion zone and "build your own" with asphalt polygons.
Your own custom airport will suppress any of X-Planes "default" airports, so if you see the runway in the wrong spot after adding it, you placed it in the wrong spot.
It sounds as if you have created the airfield, but now you can´t move it? I suggest you watch some tutorial videos on WED or OE, because it sounds like you are missing something very basic.
Good luck, Jan