I don't have any clear guidelines for that, dealing with coordinate systems can be quite complicated. Since this is very site-specific and your file is not among the common MEG file formats, I won't be able to help you much with this task.
The easiest would be to ask the Elekta/MEGIN technical support for help in adding this information to your .fif file, and then process your modified file in Brainstorm. If you are also using MNE-Python, this is also something you might be able to do from there, and then save a new .fif file.
If what you are expecting to do is to add the extra digitized head points in the Brainstorm data structures in order to be able to run an "automatic registration based on head shape": you need to find a way to convert your digitized head points into the Brainstorm SCS coordinate system, and add them with the correct format in the HeadPoints field of the channel file.