When you set up a new Flex Project in Eclipse (either FlexBuilder 3 or the plugin), the new project wizard asks you if you want to use a remote object access service, such as LiveCycle Data Services (LCDS). You can use the same option to access BlazeDS services running in a J2EE server. It requires that you have your BlazeDS server running, because the next step asks you to enter the root folder and root URL of your server.

If you want to be able to compile your Flex project without the server running, you can get around this.

If you look at the documentation for the mxmlc compiler, you'll see that the context root and the location of the services definition file, services-config.xml (which are the two things the wizard is really after), can be specified as command line arguments. SilentWalker talks about using this with the Flex Ant tasks in his blog.