Since a few weeks, Apple doesn't accept uploads of binaries from within iTunes Connect but only while using Xcode Organizer or the Application Loader. Here is a brief overview of the submission process.
When a new application version has been created, at the end of the process, it becomes in a state known as "Waiting for upload". At this stage, the developer needs to use a tool in order to upload the actual binary of the finished application.
From within Xcode's Organizer, there is a button which allows you to submit the binary. When doing so, the built and archived binary must be selected then "Submit Application to iTunes Connect..." button clicked.
The other way is to use the Application Loader from Apple. This tool is available from iTunes Connect main page. Be sure to use the latest version. At this time, version 1.3.1 was the latest one.
Once started, the first step is to select which application to submit. The drop down list is built from what is in a "Waiting for upload" status on iTunes Connect web site.
Then, a confirmation is presented in order to confirm if the application has been tested on iOS4, the latest version of iOS.
Then, we select the exported application binary (pay attention to the provisioning profile being used to export the archived app. You must select the iTunes distribution provisioning profile).
Next, all the details of the select application is presented and this is the time to actually pick the binary file from your local file system on the Mac.
Then, we click to send the file to Apple.
Depending of the size of the file, this process can be quick or longer.
Final validation are made by the Application Loader.
This complete the upload process.
Going back to iTunes Connect to refresh the status, we now get "Upload Received".
The next step will be to wait for the review to start.