You’re missing something.
If you do a search in these forums on footnotes you will discover vast, voluminous, gargantuan, nay stupendous quantities of discussion on footnotes: their use in Scrivener and the work-arounds that people in virtually every academic discipline have found to deal with your very problem. For example, take a look at this thread that appeared today: Scrivener for scientific writing?. That should start you on your way, I think.
Dave