All that "Puppy" is, as well as the others, are just recommendations for that price point. If there's a different part that you want to get that fits the build (i.e. a different case, or you think you want a better graphics card or CPU, etc.), then by all means go for it. As far as cases go, the Phantom is a fantastic case, however I would probably go for a Phantom 410 for your first build (the mid tower version, where as the regular Phantom is a full tower - much bigger).
*EVERYTHING* in a computer is keyed, it all can only go in one way. Depending the case, you may or may not have to screw things in, it's all in how the case is designed as most these days are tool-less. The case will probably come with motherboard installation instructions and the motherboard will come with instructions for everything else. If you get an after-market CPU cooler, it will also come with instructions. So, in short, just read the instructions