Hi,
I see this post is from February so I imagine you have resolved the issue, or something else has changed in your environment, however we have an FTPES connection to a third party (we have AE10 and RA_FTP 3.1.1) and I didn't need to import any certificates to get this to work. The CONN object is the default for an FTPES connection other than entering the host, username and password.
I use Filezilla to test connections before building them in Automic, and when I connect to the site I am prompted to accept the certificate; however this doesn't appear to affect Automic's ability to connect.
Hope this helps someone.
Phill..