Answer
I'll answer my own question.
After much trial & error, I've found out how to make the images save to a folder in the root of the site.
If the site is at /public_html/websiteName/ on the server, and you want it to save images in
websiteName/images folder
you need to point it to
/../images/
in the Upload Director under Global File Upload Settings
WebAssit really needs to document this sort of thing better - after all, we're paying you to save us time in our developing sites.