Are you using WTP plugins with eclipse or simply eclipse. If in case you are using simply eclipse, then there is no way to configure your App Server with it. However, you can still compile your servlets in Eclipse and get it running on App server. This can be done parallely. All you need to do is following:
1) Create a new Java Project
The structure should be:
2) Make sure that you have changed the default classes folder from <proj>/bin to <proj>/WEB-INF/classes when creating the Java Project.
3) In order to compile Servlets, you will require the servlet.jar file. You can find it in the lib directory of your server.
4) So in order to use it, Right click on Project and Click Properties in Eclipse. Then select java Build Path from the available window.
5) Click on Add External Jars button and browse through the Appserver lib directory to locate it. Click Ok.
6) Now your App Server requires information about your project. its pretty easy. I'm using Tomcat here and advice the beginners to use it. Go to the the conf directory of Tomcat. Here you will have to create an xml file MyAppServerProj.xml
7) The contents of file would be <Context path="/myproj" docBase="D:\MyAppServerProj" reloadable="true"/>
8) By making reloadable="true"., you can perform hot deployment.
10) Once you have compiled your code in eclipse, start your tomcat. And you are ready.