Compare files between ISM Source to destination
you may be able to use the dynamic linking of a folder. I have never used that. If you open the ISM, got to files, then drag and drop a new folder into you project, you should see the pop about dynamic linking.
I prefer to know what is intended to go into the MSI/ISM and add them as needed. That way i can set up the feature hierarchy properly and create new components for each file when needed. I can then set the component attributes to extract COM info at build, .NET settings etc.