The current WowzaMediaServer service script exists in /etc/init.d
You should be able to create another script like that (so clone with a different name
such as WowzaMediaServerInst2)
then edit the paths in the variables so it points to your second instance.
While logged in as root (or using the sudo command), you should then be able to start and stop the service with the commands:
If you want to add that service to the system startup/shutdown sequence
service WowzaMediaServerInst2 start
service WowzaMediaServerInst2 stop
then the following command should work:
Should do the trick.
update-rc.d WowzaMediaServerInst2 defaults