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To begin an online game, the commissioner must start a new game as he normaly would. However, on the "Set Up Your Manager" screen, he needs to add a manager for each human player in the league, and assign them to teams. He should also give them a temporary password.
Once that's done and the game finishes setting up, he needs to go to the savegame directory and zip/rar/compress the entire directory into a single file (the Mac and PC files are interchangeable, you can have a mix of people using either platform in your league.) This file then needs to be uploaded to a site where all owners can download it (filesharing sites generally work best, as the files can be large.) Once each of them has it, play begins.