All binary submissions to iTunes Connect must now be uploaded using Application Loader either through Xcode's built-in App Submission process, or directly using the Application Loader software. This offers a significantly improved experience over uploading through iTunes Connect, including faster uploading, a more stable connection, and early validation warnings. Make sure the status of your app in iTunes Connect is Waiting for Upload before you submit your binary.
Read the Distributing Applications section of the iOS Development Guide for more information about preparing your app for submission to iTunes Connect.
Registered Apple Developers can also download and watch these session videos from WWDC 2010 to learn more about using Application Loader for binary submission: