When you are using the PGP Desktop email proxy for encryption, when you hit the Send button in your email client, the email is sent to PGP Desktop for encryption, and then after being safely encrypted, it is sent to your email server for delivery. Incoming encrypted email is sent from your server still safely encrypted to PGP Desktop, is then decrypted, and then sent to your email client. The presence or absence of SSL encryption has no effect on the secure PGP encryption.