I've been programming guis in MATLAB.
From what I've seen GUIDE makes programming guis quite convenient. As you said you actually don't have to bother about programming any buttons etc., it's just arranging the buttons and filling the m-files. Within buttons you can handle visibility by setting the property 'Visible' to 'on' or 'off'.
I tried both approaches: Manually writing the gui and writing it using GUIDE.
I had the impression that you really just have to get into it. Once you got the concept of handles (that's the main thing with matlab guis) you've got it.
Try to program a simple gui first, don't start with your project. Get a hold of how handles and the inspector work in MATLAB and how you can set properties of values. Figure out where you can store data within the GUI and how to retrieve it in other windows (pass handles between windows).
I guess that's about it! Programming guis in MATLAB can be hard to begin, but it's pretty straight forward once you figured out the things I mentioned above.
