Well to begin with I would highly recommend you do NOT install Exchange 2007 on a DC. Exchange 2007 on a DC is NOT a supported configuration with Microsoft. Here is a good guide for you.
You have a lot of planning to do depending on how many mailboxes will be homed on the exchange 2007 mailbox server. There are three main server roles with Ex2007 which you need to plan for. The Client Access role, the Hub Transport Server and the Mailbox Server. All three can go on one server, but if you have a lot of mailboxes you will want to use separate servers for these roles. Our organization has two Client Access/Hub transport servers, and the two Mailbox server roles are CCR clustered servers for high availability. There is a lot more to Exchange 2007, how it runs, and the planning for it can be quite complex. Happy reading and planning! Once you have it in place you will be very happy with it, as are we.
As a hard copy reference I recommend “How to Cheat at Configuring Exchange Server 2007: Including Outlook Web, Mobile, and Voice Access” by Henrik Walther

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If you absolutely have to limit yourself to using two servers, then one option would be to configure your new server to act solely as an Exchange 2007 server (with the mailbox, client access, and hub transport roles). Once you have done that, you can move your mailboxes to the Exchange 2007 box, and then uninstall Exchange 2003 from your old server.