The main image on the eBay listing will be the first image in the listing template. You can set the main image by changing their order.

When a new listing template is created, the image which is marked as 'IsMain' on the Stock Item will be set as the first image in the template, followed by other images, and then by images from extended properties.

If the image order is incorrect on eBay, please re-arrange the images in the listing template and 'Update' it.