The slaves and masters files in the conf folder are only used by some scripts in the bin folder like start-mapred.sh, start-dfs.sh and start-all.sh scripts.
These scripts are a mere convenience so that you can run them from a single node to ssh into each master / slave node and start the desired hadoop service daemons.
You only need these files on the name node machine if you intend to launch your cluster from this single node (using password-less ssh).
Alternatively, You can also start an Hadoop daemon manually on a machine via
bin/hadoop-daemon.sh start [namenode | secondarynamenode | datanode | jobtracker | tasktracker]
In order to run the secondary name node, use the above script on the designated machines providing the 'secondarynamenode' value to the script