This article is old (2002) and can't be followed literally anymore. But it provides a great conceptual overview.
Steps when deploying manually:
1) Jar up your ejb project
2) Create the ear - look at the JEE tutorial if you don't know the format of an ear
3) Upload your ear to the server you will be using to deploy
4) Deploy it directly which will run ejbdeploy (or run ejbdeploy at the command line first if you want the stubs/skeletons created before you deploy)
I recommend using Ant for steps #1 and #2. While it is possible to do the rest in Ant, it requires you to have WebSphere installed on the machine running the build.