I use to draw scraps over a .xvi exported background. So I generate .xvi file, import it in xtherion as a background image and draw scraps over it.
Sometimes I need to re-generate background (for example to add new branches). If I do that and re-open th2 file I see the background is no more aligned with scraps. I use to manually edit the .th2 file and align it by changing the xth_me_image_insert directive.