Current best practice (based on RTM version) is to retain Exchange 2003 server(s) for public folder management. RTM only provides shell access to public folders, whereas SP1 should bring back a GUI for PF management.
Additional PF databases can be created by following technet.microsoft.com/en-us/library/bb123687.aspx
(if you didn't tick the legacy box during installation).
One option I have seen with customers is to have the IOREPL run between 2 Ex2003 servers, and then in the new org have the ex2003 server replicate onto E12 PF stores. This follows the best practice and allows PF management via a Ex2k3 GUI.
(the one potential catch of course is that you need to forestprep with E2k3 before you install E12)