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FTPS client - need to import root certificate

Okay I'm trying to help out a coworker here and just don't have the time to mess with it this week... so I'm being lazy.  Please note that I'm an expert in PKI here - I just don't have the time to mess with new software for a couple weeks.

We are looking at an FTPS client/server for a new rollout.  Right now working on filezilla server and either filezilla client or turboftp client.

We need to use our own certs - using a self-signed one is not an option.  We got the server software set up ok to allow our internal CA issued cert by specifying the pfx in pem format and the .cer file in base64.

However, client connects and we get the certificate message from both clients stating that it can't verify the ceritificate because the root isn't trusted.  I cannot for the life of me find where the root cert store is in either client software to import our internal CA's root for testing, much less determine if our public cert vendor is included in the default store or not - if Comodo is in the store for either of these then that's fine I'll just go straight to a prod cert for testing.

To sum it up nicely:
How do I import a root certificate into Filezilla client or TurboFTP client on Windows 2003 Server?


If you can't figure this out, I am more than open to other software that is easier/better to work with - both in general and in specific regards to ftps.
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Accepting my own answer for filezilla portion.  Turboftp is still outstanding, but will research that further on my own when i get time.