You wouldn't want to encrypt the CC number with the security code. It makes it easy to discover the security code if you can get the CC number, which isn't so hard to do. In fact, unless I'm mistaken, it's not allowed to use the CVV for anything. But basically, if someone is able to get the CC number, then it's merely a quick check of the possible security codes, which is small in number. Granted, I understand why you want your credit card number encrypted using user encryption, but instead of using the CVV, you might try using something else, like their password.
Storing the CC number in an encrypted format is fine, however. You want to be able to retrieve that information at a later date, after all. Should a user want to make another purchase, they really shouldn't have to enter their CVV all over again.
Granted, this all assumes you have to handle this. An even safer way is to use the gateways capabilities. Many of the option to create rebillable transactions. You send over the specifics, and they handle the rebilling for you, and you don't have to store anything of the users.