Or it might be a stack with an actual user > interface (eg checkboxes etc) so that when users edited the preferences, > they would actually be editing the preference file itself.
This is what I do. All you need to do is to set the stack files of your standalone stack to include the preferences stack. Note if I'm also creating a custom file type I often do this too. It saves a heap of mucking around every time you open and close a file and if you use few images they are usually very small files too.
