This only pertains to Shopify, Etsy, and eBay.
If you want to add/delete/change the variation images for your listings, you will need to go to the Edit Listings page for that listing. You can do this by clicking on the cog located under the eBay/Shopify icon. Then, click on Action and select Edit Variation Images.
Doing so will take you to this page. See descriptions directly on the image.
Once you've made your changes, you can click Save Changes at the bottom. That's that!
To give the previous image more context, I've provided a screenshot of the Variation Names/Values for this listing.