I contacted Squarespace Support and they provided a helpful answer, which I expanded open by organizing my scripts onto a single page:
Go to Page Settings and Disable the page [optional]
Add a Text Block
Click Files on the Link menu
You can right click and ‘Copy Link Address’ to make sure you have the correct URL
Go to your Code Injection (either the Page’s Code Injection or your site-wide Page Injection) and insert the code:
No need to link scripts via Dropbox or include the entire script in the Code Injection.
You can use this to upload any file as well, but most other things have a place (CSS files and image get uploaded in the CSS Upload File area, etc.).
Source: Creating a Text Link