You can't. Custom metafields are not supported via the product CSV import option in the Admin.
If you're already using PHP to create the csv, why not just push the product directly in via the API. You can then include the metafields in that call.
If you are open for an app suggestion, then you can import custom Metafields using the Excelify app - just use the same Shopify CSV file, and add the Metafields columns to it with the column names like "Metafield: <namespace>.<name>".
For example: "Metafield: custom.length".
More about importing Metafields, here: https://excelify.io/shopify-excel-import-export-detailed-documentation/shopify-metafields/
If you need any help with that, contact us here: https://excelify.io/contact-us/