Thanks for the info. I didn't explain my problem properly so let me try to summarize it.
I'm trying to automate the manual process of going into the IIS management console, selecting my FTP site, selecting the "bindings..." option, and finally selecting the existing certificate from the dropdown. I keep calling that "binding a certificate to a site" but I guess that's confusing.
I am able to do it through a batch file for the website, I just can't seem to make it work for the FTP site.