Walk behinds are one of the weaknesses of AGS. It's incredibly difficult to use the paint tool, so I'm not surprised.
You can paint your walkbehinds comfortable with Photoshop, Gimp or Aseprite as extra layers of your backround. Export from the tools mentioned can be automated with scripts (all these programs can be controlled via API) and Import to AGS can possibly also be done with API commands (or not?). I think the effort always depends on the skills...