Your question does not seem to be asked the right way.
It would be extremely long to guess what you specifically need because there are many different cases involved.
WED allows you to place several types of elements on a map and export the result so that it can be displayed at the right place in X-Plane :
On export from WED, the locations will be saved inside :
-The apt.dat for objects (.obj) and other elements taken from a "hidden Laminar Research library"
-A .dsf file per tile of 1x1 degree of latitude x longitude.
One .dsf file created by WED will decribe the location of objects and other elements found in :
-Laminar Research library
-any other kind of library
-local scenery pack folder
By "other elements", you should understand .lin, .pol, .str etc... for further explanations, google "x-plane file format specifications".
Before modifying an .obj file, always check the copyrights.
If you want to import a .obj file to modify it, you might need to edit it with a text editor if it has not been exported the right way. Send your .obj file so that I can show you.
You will then need to install :
Blender 2.49b (can be installed side by side with an earlier version)
Xplane2blender 3.1 (and not any earlier version) : to be activated inside Blender 2.49b.
Import your "x-plane .obj", save it as .blend.
Modify this .blend file with the latest version of Blender where you have installed the latest version of Xplane2blender before export.
Read all the tutorials and documentation coming in the various downloaded packages, check all available youtube tutorials, there are many. It's a long and hard work, and it is probably better to create your first objects before you start modifying objects made by others.
All the best with that. Also check forums on x-plane.org, which is a more relevant place to ask questions related to development.
To sum it up, WED does not create any .obj file, it only allows you to load them and place them where you want, on a 2D surface which is the surface of the Earth.
If you want to import a .obj file to a 3D editing software, you have to import it from that 3D editing software. I took the example of Blender, but there are other possibilities which I do not know. Beware, x-plane .obj it different from wavefront .obj.
This is why you need to install an addon in your 3D editing software before being able to import an x-plane .obj file.
I hope this is clear enough.