The first build we created with Emscripten used a default HTML shell file. If you have a website, this is probably not the way you would prefer your web page to look. You would probably prefer to design your look and feel using CSS and HTML5 specific to your design or business needs. For instance, the templates I use for my websites typically include advertisements to the left and right of the game's canvas. That is how traffic to these sites is monetized. You may choose to add a logo for your website above your game's canvas. There is also a text area where Emscripten logs output from printf or other standard IO calls. You may choose to remove this textarea element altogether, or you may keep it, but keep it hidden because it is useful for debugging later.
To build the HTML file based on a new shell file that is not the default Emscripten...