Admin of Confluence

I am completely out of my element, I was hired to admin windows server 03 and a few workstations, most of my experience is with deploying/engineering networks, however now I have to set up confluence. I am completely new to java, tomcat, and the bunch. I have been able to set everything up for basic use as well as basic access from anonomyous users over the internet,using mysql for the database, all in all it is functional, now there are two things that are a bit overwhelming, security and design for the wiki. Anybody familiar with this stuff?