Razor,
The LOR is a separate stream that the current Atlas pilot uses on our company web site, but the process now brings your PAQ (which has questions asking you if you have a sponsor) and the LOR together. This allows the HR folks to review your resume/PAQ and use the LOR to elevate your application closer to the top of the pile for possible next step.
An LOR can be sent in at any time by a friend and the system in place is sophisticated enough (!!) to still be able to bring (match) the two documents.
Good luck.