I have a friend who mains Puff, so I can offer some general advice against her.
Basically, you'll want to be patient. For the most part, you'll only be able to get single hits on her, especially as her percent goes up. She's super light, super floaty, and has ridiculous air speed, I've had her pop out of Ike's jab combo before, and his normally super reliable Up/Down throw combos stop working after 30%(or somewhere around there). Point is, the key to beating Puff is patience. Space her out and play some intense footsies, get your pokes and punishes in when you can, don't be too aggressive, and avoid challenging her in the air (they will have to land sometime) If you can keep that up, you will eventually get the KO. Sorry I can't offer more specific advice, I'm mostly a lurker who plays Roy for funsies.
tl;dr play lame win game