The reference image has to be the wide field one. That is, you want the narrow field image registered over the wide field. Otherwise registering these images makes no sense IMO.
No, you don't have to register 40 images manually:
1. Select one of the wide field images as your reference image. Call it R.
2. Register all wide field images against R. This can be done in a single StarAlignment instance, by selecting the corresponding reference and target files.
3. Open R in PI and define a preview covering roughly the area around the bubble nebula.
4. Reset StarAlignment, set Maximum stars to 200 (Star Matching section), and select R as the reference view.
5. Register all narrow field images against R. Again, this is a single StarAlignment instance.
Let me know if it works.