Dsmash, dtilt, dash attack, and fsmash on block against Puff are punishable by Rest [as are other options like badly spaced aerials, but those 3 are notable]. Be very careful of those options. Some won't punish it [they'll opt for other options out of comfort, don't know it, or will opt for other options to try to condition you into thinking it's safe so they can land multiple rests if you keep doing it] but good ones will.
Up+b can be punished by rest if she falls out, if she SDIs out, and/or if you don't edge-cancel it [and of course if you whiff]. Be careful of that as well.
I'm not sure how reliable this advice is, but I know some pretty good Puff players said Samus's best strategy is to kick Puff away and charge charge shot [the way you might see Clouds try to get limit in Smash 4, if you're familiar with the game]. This will let you get access to charge shot more often during the match, and charge shot is extremely useful against Puff [25% fresh and fully charged, KOs early, connecting one lets you get progress on another or stage control at almost every percent if it doesn't seal a stock]. It's something I tried vs Puff the few times I tried the MU and it seems to work fine if you're comfortable with the endlag on charge shot cancelling.
Puff can duck Samus grab. She can't duck extender with homing on [from what I know], but grabs are thus risky vs Puff too (and extender has its own problems).
Good Puffs will come offstage against you to intercept bomb recoveries... be ready to be tricky with your recovery and be prepared to throw out aerials or avoid her while trying to get back onstage. Her airspeed is better though, so gimps are quite possible even if you're recovering pretty smartly.
No actual advice on fighting neutral from me [besides the one part about charge shot], but I imagine this is the sort of thing you'd want to put in your phone if you're worried you'll be forgetful.