Hello zetpap,
Actually the last and before versions was hard to customize.
It's important to not customize file will be updated (plugin, WP core, etc.).
That's why, the new version use more CSS id & class to permit to customize any buttons (add to cart, payment, checkout) using the WP theme CSS (style.css) to avoid any plug-in modifications.
You have to just cut and past your CSS modifications at the end of you theme style.css file.
@niksag : don't click on update to not update ;-) . But it's better to use theme CSS to customize it. If you upgrade Wp or any plugin, old file are removed and new file replace it. This is the WP upgrade process.
I hope this help,
mike