1. To create a custom theme in cs-cart, first clone the basic theme to avoid modifying core files. Then create a new preset to customize colors, fonts, and other design elements before saving it.
2. Next, create a new layout by cloning the default layout and rearrange blocks as needed. Settings for individual pages can be customized in different layout tabs.
3. Making a new preset and layout allows full customization while keeping the original templates as backup if needed. The process involves cloning, customizing presets and layouts, and saving changes.