Bungie Pro is a file storage and sharing solution that is not in any way, shape or form integral to your Halo 3 experience. Simply put, it's the expansion of storage for your files, these could be Films, Clips, Screenshots, Map Variants, Gametypes or some combination including some or all of the aforementioned. The default File Share for players is six files, Bungie Pro expands that file share.
That File Share is stored on Bungie.net in both standard and expanded forms. Both the standard issue File Share and Bungie Pro both allow players to tell their 360 to download files from Bungie.net.