While it's always possible to go on Cogniview's site to upgrade your PDF2XL license, you can also upgrade from within the program itself.

The Upgrade Wizard, accessible from the Start menu, gives you several options:

In this screen you need to enter your payment code and email address.
The payment code is the one that belongs to the upgrade, and not the same one you used to activate PDF2XL originally. You can find it in the purchase confirmation email that you received after buying the upgrade.
The email address is the one you provided when you purchased the upgrade.

Much like in the activation, if the computer is connected to the internet then PDF2XL can connect to Cogniview's server and apply the upgrade automatically. If your computer is behind a firewall that blocks this kind of operation, you can also apply the upgrade via Cogniview's website.
In case none of the above methods worked, or your computer just isn't connected to the internet, you can apply the upgrade via email or fax.