The structure of an EC2 startup package mirrors the structure of Wowza, with /conf and /applications and /lib folders. You configure these folders in the startup package in the exact same way you would a Wowza server, so it's very easy as far as that goes. The one issue is 16kbs limit on the zipped package. To get around this if you have large jar files that need to go in the /lib folder, you add a Download tag to the startup.xml file, then put the jar files on a web server. You can zip it up and have it unzip.