I successfully generated an SSL certificate with the Certify The Web app intending to use in for an FTP server's web UI. But, in order for this web server to accept the certificate it also wants the certificate's password, which of course doesn't exist.
How do you deal with this?
Thanks,
Kenny
Welcome to the Let's Encrypt Community, Kenny 
Per the words of the developer of Certify the Web himself, the default PFX password is blank (meaning empty).
Documented specifically here:
Additionally:
Thanks Griffin. I tried to download CertSage, but I couldn't find a download link.
How can I get a copy?
It's still in the final stages of testing and not yet fully released to the public. Given what I've read about your configuration and requirements, CertSage likely isn't the best choice for you. If you can't get Certify the Web to suit your needs, I highly recommend certbot using the standalone authentication method. You can user the --pre-hook and --post-hook parameters to shut down and restart your Wing FTP server, respectively. Since the standalone authenticator spins up its own temporary webserver on port 80, it will handle the certificate acquisition process for you.
You should be able to export the cert generated by Certify The Web into standard PFX format.
From there you can manipulate that output file to any other format (if needed).
If the Web Server requires a password...
Then export the cert into PFX format and add a password to that file (during the export).
Then add the exported (and password protected) PFX file into the Web Server.
[sadly, most of that seems to be a manual process - I would look for something fully automated]
Certify outputs and stores a PFX by default (and configures IIS automatically according to matching domain/hostnames in existing IIS bindings). There are additional Deployment Tasks for other service types/certificate formats. Which "webserver" are you using?
If you want the PFX password set you can specify it under Certificate > Advanced > Signing & Security, this is a stored credential that can be re-used across other certificates if you want to have the same PFX password for more than one cert. It can be centrally managed (replaced etc) via Settings > Stored Credentials.
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