You don't have to cover up anything, if you right click on the system device and select properties, then go to settings, you can hide or unhide everything but the very bottom buttons. I personall don't hide them, I just created a copy of an empty button and placed it over the one that says tools.

And if you need to manually position your panel or button for a better fit (like if you created your own shuttle buttons), double click the button and then select the dimensions tab.