I am assuming that you need to put it in the startup applications, but i am not completely clear on how to do this.
Go to System → Preferences → Startup Applications and click the Add button. You'll see something like this:
The name and comment are just for you to recognise it in the list of startup applications
The command for empathy is just
If you're unsure about a command you can start the application, open the System Monitor and check the Command entry in the process list.