[CentOS] mysql secure installation and multi mysqld

If you adjust the my.cnf file to make separate instances of mysql.....

How would you go through the mysql secure installation? Is is possible 
or must it all be done manually
for each one?

is it possible to make each one of those instances a replicate/slave of 
a different master
(thus a backup mysql server in a way?)

working on this now, but having issues getting it to work.
(centos 6)