You don’t (generally): WorldPainter is a tool for creating maps from scratch. It only cares about terrain and will destroy man-made structures in chunks where terrain is touched. Technically it is possible, but it is not recommended or supported.

The exception is to transform terrain far outside of your build areas, and export with read-only layer over the build areas. This method will require import/exporting to the exact same minecraft version and possible leave a visible seam along the transition line. Its only recommended for very experienced worldpainters.