You can safely set up BES but do so on a separate server and do NOT install Outlook on this Blackberry server. RIM strongly recommends this.
All the BES is doing is monitoring mailboxes you set up. It polls the appropriate mailboxes and send messages to the respective handhelds. It also takes messages from the handhelds and sends them out through the mail server as thought the user was connected using Outlook or OWA.
Assuming that you are doing an inplace upgrade there should be little to do with the BES but I can’t say for sure. Check out the RIM support pages as I am sure there is a FAQ about your upgrade scenario.