I use SSI for my site, which has tons of sub folders. Is there a way to upload the txt files into my main folder and link to my others instead of uploading the txt files into each and every folder I have? It's starting to get a bit time consuming....

<!--#include virtual="http://domain.com/blah/ssi.txt" -->

Use that instead of include file, and put the entire URL in. It should work with that.