I did some of this back when. If I remember properly, if you merge two files and the group names are identical, one will replace the other. I think I have seen both effects: two essentially identical groups on top of each other and the new replacing the old. I just do not remember what produces each effect. Experiment. Learning all the options of the tool can not hurt. But combine is straight forward. Open the add on parts file and delete any extra groups and save it. Open the base file and delete anything that needs it, then open the add on file, check the merge box , then write. You will wind up with one big file. save it and then the fun begins with the CR2.