Feed The Beast Server

Hey guys, i'm trying to run a FTB server and i was wondering about something. ok so when you load the server originaly it runs out of the same window that a normal minecraft server runs out of. I want to run it out of terminal on my mac. I got it all programmed to run out of my terminal but i have one problem. when i start up the server it runs it terminal and in the normal minecraft server window thing. they then each notice that the server is running in the opposing window and then proceed to shut down. I want to know if anybody knows how to deactivate the normal minecraft server window thing so that my server can only run out of terminal. Thanks guys