Yes overnight you would use PUPD for each night waking. However, make sure you decide before you go to him whether this is a 'feed' (ie 4h+) or 'not feed' waking. If you are feeding, do it straight away and put him back in bed (ok if he falls asleep feeding for middle of the night feeds), but if it is a 'not feed' waking you use PUPD and see it all the way through to him falling asleep, even if it takes you past the 4h cutoff. That way he doesn't learn that protesting long enough gets him a feed. You can then feed him at the next waking.
For naps, you would use PUPD for 45 mins max. Take a short break, low key A time, feed if due and then try again for a nap earlier than you would have done. If you keep him up until the next scheduled nap time he will be super-exhausted and not in a position to learn. He will skip naps - that's normal when sleep training, but with consistency the OT should start to work in your favour because he will have to sleep at some point. When trying to resettle from a short nap, I would try for 15-20 mins max and then just move on with the day, bringing the next nap earlier. Life is too short to spend in a dark room with a screaming baby!