A lot of people will design in the new Pro builders or Cornerstone directly. Some will mockup a comp in Photoshop or Sketch and use it as a template for the final layout/design in X/Pro. Some will start with a Demo in X and customize from there. It all depends on your personal design style or skillset. Those with experience in traditional web design/development will probably start in Photoshop. Those with less design skills will usually start in Cornerstone or with a demo. In the coming months, Pro will gain the ability to import/export templates which will probably mean more third-party ones will start appearing online as well.
I feel most productive when I have something to reference, whether that is a Photoshop comp or something sketched out. Sometimes if its just a single new page, I will just use Cornerstone and play around.
In most cases, its usually best to setup a child theme before doing any customizations. By using a child theme, you’re free to make any changes to the CSS/PHP without the needing to add them back after each update, as WP updates replace the full theme/plugin folder. If you make changes to the theme CSS or PHP it will be lost at every update. Its also considered a best practice to not alter core theme/WP files directly.
To set up a child theme is not much different than installing a regular parent theme. In your Themeco dashboard there is a link to download a child theme for both X and Pro. Just install that as you would any theme and activate it. That’s it. You can also create your own, but that’s a tad more involved (still pretty simple though).