To have Xcode generate your certificates for you, open the Organizer (Window -> Organizer or ⌘⇧2), and select Provisioning from the list on the left. Then, in the lower right, click Refresh. Xcode will prompt you for your Apple ID credentials.
If no Development/Distributions certificates are found, Xcode will prompt to start the Certificate request process for you.
To do this manually in the portal, login to the Developer Portal and click on Provisioning Portal. From there, follow the instructions on how to create a Certificate Signing Request (CSR) from Keychain and upload it to the portal to have your certificates created.