Getting it up and running on Squarespace isn’t as hard as you might think.
Note that the downloaded .zip will include bigfoot-default.css. I removed the -default from the filename before uploading to Squarespace. The site will look for bigfoot.js and bigfoot.css.
Once you’ve edited the files, you’ll need to upload them to your Squarespace site. The system doesn’t have a media manager like WordPress, but files can be uploaded easily enough.
Note that if you’re already calling jQuery already in your head, you can skip line 1 of that Gist.
If you hit Save on the Code Injection module and refresh your page, everything should be working smoothly. Remember that Squarespace doesn’t support Multimarkdown, so to add footnotes to your articles, you will need to use HTML.