No worries, I just wanted to make sure you saw what I was saying. You are also more understanding than most users too, so don't worry about it.
The easiest way I would solve this is to yea, search for the images you want. If in this case they are the images with 1 attached to them, then search them up in the folder and move them. I would personally also use a program called Métamorphose 1 v 1.1.2 (version 2 has a slightly more complicated UI), and use it to take out the "-1" portion's of the file name. You can then move them to the games box art folder or where ever you want. Since they should have the same name as the front box art images now, you can either replace the existing ones so that it is mostly cart images or don't have the cart images overwrite the box art and then you will have it be mostly box art. Either way, the result should be less holes. It's not a nice solution granted, but it is a solution before features like Tiered Images can be implemented.
http://file-folder-ren.sourceforge.net/index.php?page=Download Any other file renamer will work, this is just the one I use.