I admit that I had a little trouble figuring out what you were talking about, but I think I'm figuring it out (some).
The best thing you can do is ask for an experienced staff member at PetSmart to discuss with you the dog's needs. Experienced is the key.
They may not let you do what you are hoping for. I actually don't think that your puppy CAN indicate to you what he will prefer. And he has to wear a collar and leash whether he likes it or not. That should be non-negotiable. The earlier you start it, the better.
Not every dog is interested in sleeping on a dog bed. It's more about making sure he "fits" sizewise in it, and training him to sleep in it (not allowing him to sleep on your bed.)
Your guinea pigs and the tunnel really have nothing to do with this. (I know, having had both...)
You really need to read up on dogs and humans and the relationship between the two, and you and your family being alpha over the dog. You should REALLY consider obedience training - it will educate you as much as your dog, and make for a much happier dog ownership experience.
Good luck,
Dawn