If you have multiple images that need to be assigned to a product, you will need to assign one image as the featured image/thumbnail, and then assign the rest of the images as the product gallery thumbnails.
Below is a quick function that can achieve this for you:
function so_upload_all_images_to_product($product_id, $image_id_array) {
//take the first image in the array and set that as the featured image
set_post_thumbnail($product_id, $image_id_array[0]);
//if there is more than 1 image - add the rest to product gallery
if(sizeof($image_id_array) > 1) {
array_shift($image_id_array); //removes first item of the array (because it's been set as the featured image already)
update_post_meta($product_id, '_product_image_gallery', implode(',',$image_id_array)); //set the images id's left over after the array shift as the gallery images
}
}
Assuming you have an array of image id's, and the id of the product that you want to attach the images to, you can call the function above like this:
$images = array(542, 547, 600, 605); //array of image id's
so_upload_all_images_to_product($product_id, $images);
If you are working with a massive array of product images, or you are very serious about micro-optimisation, you can use a combination of array_reverse and array_pop instead of array_shift.