Excludes and Flattens in SbuilderX

Hi
Looking for some advice as I'm completely stumped.

I'm trying to flatten and exclude the airport and area around my first airport update but i'm having a real hard time with it.
I'm not sure if it's an Sbuilderx issue or me,or possibly both.
I'm running sbuilderx3.14 64bit version and trying to update an airport in P3d v3.2.

My runway sits at the correct altitude, real world elevation of 22 ft which was set within ADE, but when I run the sim my runway sits above the sat image and surrounding area .
I tried creating an exclude airport boundary area and set that for the same height as the runway which did not work at all, as the surrounding water had buildings and trees in it ,but this maybe due to

no watermask added yet?
I've tried to add an airport flatten first instead of an airport boundary exclude, but all this has done is push everything below ground level.
I am completely stumped .
Could someone possibly explain what order is the best way to go regard excludes and  flattening etc .
I should probably add  that I'm using ftx global and ftx vector and LC  and the airport is in europe so Should I run the vector configurator before trying the airport .

The only other thing I have noticed that in SbuilderX  my cvx bgl file of the polygon exclude is found in the shapes folder and not the work folder, as I've seen on some youtube videos is this correct?

Thank for any advice you can give.