They scale with the gui layer. So you can either resize your gui layer, which is fine if you aren't using it for anything else, or you can resize your keys on the layer, which is harder, but won't interfere with other things on the layer.
Either work really. It's easier to do multitouch buttons with virtual keys, but GM:S can handle 5 mouse click events at once as I recall. Should be more than enough as people generally only use two touches at once.