First, pick the cover you want to change. I'm using this one because it's easy.
Then block(or erase) the images you don't want.
You can start putting the new images in place. I find the ones I want to use before I start..makes it easier when I don't have to go through a folder with hundreds of pictures for just a few
You can crop your images if you want to now. I made the front ones square because I liked how they looked, and it made them a bit easier to arrange
Once you have the pictures where you want them you can add edges, or other touches if you like. Then all you have to do is save, and print, the new cover.
You could do this in just about any image editor, and no doubt there are lots of better ways to do it, but this is what works for me. I don't think the results are too bad :-D