Make online payments for your Amazon.com Store Card through the website listed on your bill or by following the link Amazon sent you in an email. You can also find links on Amazon.com, but these typically involve working through a few extra steps.
Once you've reached the payment website, sign in with the User ID you set up previously. Enter your password on the next page, which brings you to your online account page. On this page, simply click on the Payments button, and then select Make a Payment.
If you have not yet set up a User ID, click on the gray "Register your Amazon.com Store Card" link, and you'll be walked through registration. You can only make online payments using your ABA/bank routing number and your checking account.