Yes. The only thing you should avoid is putting the SEE database in the same SQL instance as the SEPM is using.

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/end...

https://www-secure.symantec.com/connect/forums/end...

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.