If you pay for your hosting using a PayPal subscription, you'll need to make a separate payment for your domain registration/renewal. When your domain registration is due, you will see a special alert on the Make Payment page with a link to pay for your domain renewal.
For other situations where you may need to make a one-time payment, (such as if your previous month's payment failed), you'll need to cancel your PayPal subscription in the members area under Payment Preferences by clicking on 'delete payment info'.
Once you've done that, return to Make a Payment and complete the payment for your domain registration. Once you've done that, you can return to the Payment Preferences screen and re-start your PayPal subscription.