For general advice and examples for how to create a GUI (and avoid using GUIDE), have look at this thread.
It will show you different ways to create a GUI with Matlab. You could put all that in a script, but I would strongly recommend using functions instead. Even if not talking about GUIs I hold the opinion that a script is only for debugging/designing something. As soon as you spend serious time on something and/or are planning to keep it for more than a week or so, you should consider functions instead.
