Have you added the scripts to an existing project?
Okay, first back up your project just in case. If you made any custom screens in the screens.rpy, put them in another file.
Then you need to remove the screens and gui.rpy. If you look at the original template folder, you see that they aren't there . The glitches are most probably caused by conflicting styles, like the return button's size and position being set in the template's game_menu.rpy but the original screen.rpy still has the styling that makes it the wrong colour (this is just an example idk the code by heart).