Associate the certificate to CuteFTP Pro which it will send to SSL servers.
On the menu bar click Tools > Global Options.
If you don't see SSL security click on the plus sign to expand Security.
Click SSL security.
Select the Use SSL Certificate when authenticating check box.
Click the Browse buttons next to Certificate and Private Key and select the appropriate files.
Enter the passphrase in the Passphrase and Confirm passphrase boxes.
Click Apply and OK.