Hey bobrocks95, and welcome to the forums. I'll try to answer your questions. For your first question about storing, I do it with foam also. You don't need a lot just in places to hold the game. Not too hard. For the second about the Spines. What I personally do is use the template the larryinc64 has on the site and do it in photoshop. i would have the finished 3ds cover on one page and on another I would use the "rectangular marquee tool" to outline the custom spine. Next, I'll use the "move tool" to take the custom spine and move it to the cover i want to change and place it on top. (I'm not saying this is the best way to do it. I'm not good at Photoshop and its what i found easiest)
Hope I helped.