You can start genesis from your S:User-Startup - just put two rows: "Run <>NIL: AmiTCP:GenesisSomething...." and then "WaitForPort AMITCP". You also have to set some options in Genesis first to autoonline the interface you use and not to popup the GUI.
You can also in the Genesis preferences set to execute stuff when it goes online - for example Facts. Facts doesn't seem like a very good program though, as it crashes with no TCP/IP-stack available.
/Patrik