No, it will work separately as well.
That is, if all you want to do is protect your Exchange traffic, you don't have to buy Server Edition itself. Just buy the Exchange Server Edition for the appropriate number of mailboxes.
You'll install the whole Server Edition, including the Exchange plug-in. If you enter a license file that only cotains an entry for Exchange Server Edition (i.e. no Server Edition), the on-access protection of the server file system will not work. But you'll of course have Exchange protection, and also still have the on-demand scanner and all the other modules of normal Server Edition. Only the "Standard Shield" will be missing.
Hope this helps,
Vlk