Migration to WooCommerce will convert your custom options to variations for most types of custom options by default. This process is limited to the following types: drop-down, checkbox, select box, and radio button.
If your products have more than 4 custom options, or some kinds of options are not in the supported list above, you should use the Product Custom Options plugin for WooCommerce. There's a ton of different options you can choose from the plugin, such as check-box, radio button, select box, textarea, input box, upload, date, range picker, color picker, product elements and more.
If you want to use the Product Custom Options plugin, please submit a ticket from your Account Dashboard and we'll customize our migration tool accordingly.