Ok, first a bit of perspective: S4 is useful as a "trial run" for exams as Nat 5s, in the grand scheme of things, are not as important as Highers and (unlike England) don't determine which school you go to "next" as almost all our schools go all the way through to S6.
So if he really cocks up, he can re-sit some Nat 5s in S5 (or evening S6) at the same time as doing Highers/Advanced Highers.
I believe that in the original concept of Curriculum for Excellence, Higher calibrate students wouldn't even have sat Nat 5s and should have proceeded straight through to Highers.
In practice, most schools took the decision that it was unfair on their young people to have their first experience of formal exams be the critical Highers in S5.
So look on this year as an opportunity for your ds to learn the importance of being organised, in a relatively safe environment.
I was fortunate in that ds always got himself organised - but even he acknowledges that he didn't truly realise how much ongoing study helped until after his Nat 5s.
Does his school produce a study guide or do study workshops? If they do, encourage him to do them. Ds' old school also did them for parents so that we could understand how they were learning and what we could do to help.
At this age, he does need to start learning to organise himself - but you can help in asking him if he has a study programme and what can you do to help.
Come across and pose the question again in Scotsnet - there are lots of people there whose kids have gone/are going through the process and/or are teachers.