Hi autsoldnow - product version info would help, assuming your E2K3 w/ BES 4.x? I'd definetly go with building a new Exchange Box. E2K3 on Domain Controller your asking for trouble.
Re how it all 'integrates' - BES still references a user's legacyExchangeDN assuming your new box is in the same Exchange org, you can safely move mailboxes between stores & servers (i do this all the time as i have to constantly juggle space between my stores).
I'd use ESM to move the mailboxes - as this also moves "BlackBerryHandheldInfo" folder at the root of the MAPI folder (you can use mdbvu32 to view this). Not sure if exmerge will do this.
Hope this helps.