How to add new variations to an existing listing
You can add new variations to an existing variable listing any time. All you need to do is to add your variation in WooCommerce and make sure you provide the product ID (UPC, EAN, ASIN) exactly as you did when you listed the product the first time.
Products that use a category specific feed template like "Clothing" or "Customer Electronics" should have either UPCs or EANs assigned to each variation. So when you add a new variation to a product that already exists in WP-Lister for Amazon using a category feed template, it will be added to WP-Lister and listed on Amazon automatically - if it has an SKU and either UPC or EAN set.
Products that were matched by ASIN are added to WP-Lister automatically already. So all you have to do is to add the variation in WooCommerce and click the Match in Amazon button to find and select the ASIN for your new variation. If you already know the ASIN, you can enter it in the ASIN field directly and click Update.
Brand registry and UPC exemption
If your brand is registered with Amazon and you are allowed to list new products without UPC/EAN, then WP-Lister will ignore any new variations that are added to a variable product which already exists in WP-Lister, because these variations would have neither UPC nor EAN nor ASIN.
To let WP-Lister know that you don't need any product IDs, you need to enable the Brand Registry option on the edit account page. With that option enabled, new variations will always be added to automatically to WP-Lister if the product has a listing profile assigned - unless you tick the Hide on Amazon checkbox for that particular variation.