This week's book giveaway is in the OCPJP forum. We're giving away four copies of OCA/OCP Java SE 7 Programmer I & II Study Guide and have Kathy Sierra & Bert Bates on-line! See this thread for details.
There are two ways of running Emma. One is through a main method or JUnittest. The other is on the server. (the emma faq shows how to set that up.) The server approach is useful when testing through a web app.
If this doesn't help enough, please elaborate more on what you are trying to accomplish.