To place a Pokepuff in the house, click on your Pokemon. Beside "Play" is "Decorate". There should be a tab called "Pokepuffs".
Pokemon stop by automatically when you're connected.
My question is, what are the fourth and fifth level puffs? I've been mentally categorizing them as "plain", "frosted", and "topped" from level 1 to level 3. I play games on Hard/Unlimited and get good scores, so I know I have some of the top level ones. Also, my Pokemon usually get 4-5 hearts per puff eating any of the "topped" puffs, so I'm not sure what I'm not noticing.