These files are not "in the database". These are sql database files that are in that directory. You will notice there is a data file and a log file (for transactions) for each of the databases. The master, model, msdb, and tempdb databases are sql installation specific and not related to BES. There are specific methods for moving/modifying these databases without causing ireperable damage to the sql installation. You can find that here: How to move SQL Server databases to a new location by using Detach and Attach functions in SQL Server
There is much more detail to be said of these but this is not the forum for it.
As for the mdss and mdss_dis databases, if they are your BES databases and you would like to move them, you should stop your BES services, detach them (in sql), move the files (in windows), attach them (in sql), start your BES services again.