There will never be any guides on how to protect server x.
First, you need to find out whats running on the server. Having the agent installed in monitoring mode only will assist in this. Then you need to decide what your base protection strategy is going to be. What do you want to run on this server, what don't you want to run. Who should have access to what, and where, and when?
All these types of questions need to be answered before you can decide on a strategy. When you have that strategy decided, you can begin to lock down the machine with policy.
Seriously though, if you've never used the product before, I strongly suggest bringing in some Professional services to assist you in creation of policy. They'll be able to help you create policy, and provide knowledge transfer so you can continue the process when they're gone.