For full debugging capabilities, you need two debugging sessions. One for the client, one for the server, because each JVM has its own debug server builtin. Also, if you're running both on the same machine, they have to use 2 different debug network ports, since the rule is that a port can only be owned by one server at a time.
If you connect a remote debugger to JBoss, you should be able to take breakpoints and do all the usual debugging functions on the server-side code for the EJB. To debug the client, you'll need (as I said) a debugging session to the client app as well. If you're running that app from within Eclipse, you won't need to explicitly set up a remote debug configuration, though - just start a debug session like any other app.
That's one of the strengths of Eclipse. It has the ability to debug multiple applications/servers at the same time, and it's really useful in complex setups where multiple JVMs are talking to each other.
An IDE is no substitute for an Intelligent Developer.