In order to properly create a product with variations in the WooCommerce and then customize it inside Zakeke please follow the steps highlighted in this guide.
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Create Global Attributes. Inside your WooCommerce admin go inside "Products", then select "Attributes" and create one
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Create a new product and in Product data select “Variable product”.
In the Attributes section click on "Add Existing" as showed in the image below:
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Click on "Save Attributes" and go to "Variations Section" and click on "Generate variations":
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Once you save the settings and the product you have created, you can go inside the Zakeke back-office and configure your own product.
To do so please follow this guide here > Create a Customizable Product