I'm working with a tool right now that requires me to putty to a remote host, login, run a series of commands to start an engine, open a new window (and login again) to start a different engine, then open a third window (and again, login) to actually use the tool (leaving the engines running in those first two windows). I'd like to write a shell script to automate the process so that I could just open one window, type "sh whatever.sh" and be off and running, without physically opening the new windows and logging in again. However, I can't find a command to get me from one window to the next. Any thoughts?
You can just background the first processes by adding an ampersand (&) to the command line or pressing Ctrl+Z when it is running (and then enter bg to let the process continue, more information about that with jobs).
If that's not enough, you can create virtual shells with screen or tmux.
If you've redirected X (i.e. you can access GUIs over ssh), you can also just start a new window by executing your favorite (GUI) console program, like xterm, konsole, gnome-terminal, etc.