Crystal Reports is a separate install that should not harm your Enterprise deployment if Crystal is the same version/service pack level as Enterprise. It will not install an additional CMS. It sounds like the copy of Crystal that you have is probably older than the version of Enterprise that you are running.
For example if you have Business Objects Enterprise XI R2 SP2 then you want to install Crystal Reports XI R2 SP2. I have experienced first hand an install of mixed service pack levels on the same server and I wound up with a hosed page server.