What is the negative impact of that? A clustered mssql, hosting 2 separate databases should be fine, yes?
For your intrest, you may want to look to the below link.
https://www-secure.symantec.com/connect/forums/endpoint-protection-encryption
https://www-secure.symantec.com/connect/forums/endpoint-encryption-endpoint-protection-manager-same-server
1 > Install Symantec Endpoint Encryption (SEE) first and Symantec Endpoint Protection Manager(SEPM) later, as all ports in the SEPM are configurable in case of any possible Port conflicts. 2 > As mentioned above Instance should be different for SQL DB for SEPM and SEE.
3 > Use Custom website for SEPM and SEE(By default) in IIS.