While installing BOXI R2 Enterprise, you have the option to either include the database server (MySQL Server) and web server (Tomcat) installations from the BO bundle. You can either opt for this or un check options for either or both of these depending on how you have planned your BO environment. You need to check with whoever is it who performed the installation.
Though I have not done this myself, I guess this is very much possible. If you autoplay the BO installation CD, you get an option like Repair Installation. Follow this and you can get Tomcat to be installed, configured with the existing BO installation, separately. Try this and do let me know the result.
One other option may be that Tomcat was already installed before XI got installed. In that case Tomcat will be listed in the Windows services listing (check that) but not in the CCM because it is named differently in the Windows Registry. I found an old kbase on solving that issue:
Symptom
Upon reinstallation of BusinessObjects Enterprise XI running Apache Tomcat, or upon reinstallation of Tomcat from a source other than the Enterprise XI CD, the Apache Tomcat server no longer appears in the Central Configuration Manager (CCM).
To resolve this perform the following steps:
Go to Start > Run and type “regedit”.
Go to HKLM\System\CurrentControlSet\Services, look for ‘apache’ or ‘tomcat’, and rename it to “BOBJTomcat”.
Ensure that the ImagePath value matches the new name “path to tomcat5.exe” //RS//BOBJTomcat
Open the CCM and Apache Tomcat will be displayed in the server list.
Is there any advantage for having Tomcat in the CCM in stead of the one listed in Windows Services?
No, other than the ease of being able to restart all the relevant BO services in one go using the CCM. But you could easily create a batch script to do the same thing.