Atherton was appointed in November 2020 and has since overseen a more focused strategy towards individual player development, with the aim of seeing more players make the leap from youth-team to first-team.
"I think I've looked to develop the individuals within the group," Atherton said on how he feels the youth-team set-up has progressed under him.
"I had a few ideas I threw around with Steve (Nichol, head of youth development) around adding in position-specific sessions, really getting into detail around the guidelines for success we have and starting to go down the individual player responsibility route and how we develop the individuals in the team to give them the best opportunity to get something with the first-team.
"We had a good base already. I created a coaching programme designed to be able to manipulate the sessions, work on those individuals in the group but also develop the group as a whole, make the team more competitive.
"I think over the last couple of years, especially this year, we're now starting to see that.
"The position specific sessions, the coaching programme and the guidelines for success, they've all given the lads on a weekly basis something to look at and self-analyse themselves against, to go 'what do I need to do better?', 'what do I need to work on?'.
"It gives them a better understanding as well, they're going into training and games knowing what they need to work on."
Atherton says being able to analyse games and training sessions more often has aided player development.
"We have purchased a new camera and mast that records games and training automatically," he said.
"When we upload them onto Hudl, the platform we use which we share with the first-team, they can go on and look at their individual performances and also review the opposition.
"Have a look at their traits, what were their strengths and weaknesses, what can we change when we play them next time.
"Individually, how are you going to affect the opposition, what strengths of yours will help us beat them.
"Hopefully that side has had a big impact."
Another area Atherton feels has helped progress the club's youth set-up has been an increase in self-promotion.
"Social media now is more important than ever in that you've got to be out there showcasing what the club's doing," he said.
"Over the last 12 months we've started an Academy Instagram and Twitter account which has generated a lot more interest from players.
"It's also about club recognition, you've got Halifax fans always commenting on the stories we put out, liking it, sharing it, so it's getting noticed.
"Social media does help to get us noticed with players, who will contact us week-in, week-out saying they've seen what we're doing, because we show the gym sessions we run, the guidelines to success we've drawn up, the games.
"So it's generating interest from players to go 'this is a really good set-up at Halifax'."
Atherton worked in the youth set-up at Oldham Athletic at the same time as Pete Wild and Chris Millington, and says that friendship helps tighten the bond between youth-team and first-team.
"It's massive. It's always great having that relationship with the gaffer and the assistant from before, it does go a long way," he said.
"It also helps that their background was youth development, they've got that experience and they know what it's like from my perspective.
"They know how difficult it is to get players up into the first-team.
"I love being around the first-team too because it helps with my personal development, and I get a good insight into what the first-team is doing on a week-by-week basis.
"I'm always asking questions to the manager about what have they been working on, all the individual bits they do with the players, which helps me relay that to the youth team lads.
"So I'm saying to the lads 'this is what the first-team players are being told at the minute, so if you want to be in and around the first-team, these traits are what they're doing'.
"I can say to one of our right-backs 'this is the information Jay Benn's being given, this is what he's doing to improve himself, so that's what you need to be doing within games'.
"Our philosophy is very heavily linked to what the first-team do.
"If you were to watch our under 18s play, it would be a similar structure and organisation to how the first-team play in and out of possession."
When asked if he feels there are players in the club's youth teams capable of making the step-up to the first-team, Atherton said: "It's tough to say because they're 17, 18-year-old lads.
"It's classed as your youth development phase. The lads are in there, they're making mistakes and it's about teaching them the winning mentality, so saying to them 'OK, you might be making mistakes, but you've also got to have that winning mentality because if and when the opportunity comes with the first-team, these mistakes aren't youth development mistakes, they're mistakes that could cost three points.
"These lads need to know that there is the youth development side of things but also you need to win games, be competitive and make sure you don't make the same mistakes if you get something with the first-team.
"We do have some lads who train with the first-team on a regular basis, which is brilliant.
"The gaffer is always asking for two or three lads a week to get involved in training.
"Sometimes he'll ask for specific lads to go, instead of us choosing he'll say 'I want x, y and z'.
"Once the lads go up to the first-team then they're kind of out of my hands.
"I say to them 'you've done well enough to get noticed, you've now got to put your all in to prove what you've got'.
"They've then got to prove to the manager that they're good enough to get something at the end of the year."
Town's youth team plays in the under 19s National Academy League North Division, and are also in the semi-finals of the under 19s Academy Cup for the first time, booking their place in the last four by beating Chesterfield 3-1 last month.
"I was really pleased with the lads. We've been a bit up and down in the league, we've had wins and losses, wins and losses, a bit of a rollercoaster," Atherton said.
"But the cup run, every game I've said to the lads 'look, this is where the winning mentality comes through, you've got to want to win these games, want to be competitive and work hard'.
"They've played some really good football. We've beaten Chester and Chesterfield to get to this stage, who are two very, very good sides and two very big sides in the league as well.
"To get past them is a great achievement for the lads, they've done really well."
With promotion a distinct possibility for The Shaymen's senior side this season, Atherton says the knock-on effects have already been discussed for the youth side.
"Steve and I have had conversations, and the gaffer too, about it and we're looking into it," he said.
"Fingers crossed we do get promoted and if we did we could progress to become an EPPP (Elite Player Performance Pathway) Category Four status purely because the infrastructure to from where we are now to Category Three in the turnaround space of three months is just a bit too much.
"A very well structured academy is developing below the youth team from ages nine to 15, 16, so that would take six months to a year to get the turnaround going.
But for now, Atherton is focusing on getting the conveyor belt rolling.
"We need to be competitive. We are a good footballing team, we generate very good technical players who can play football," he said.
"For me, it's going to be about being competitive in the leagues, having that mentality of, yes it's youth development, but you've got to be winning.
"The key thing for me though is getting players into the first-team, that's my job.
"Over the next couple of years, if I can get two or three lads into the first-team then that's my job done.
"My big emphasis is individual player development, but you're not going to get all your players into the first-team.
"You've got to push and strive and help those individuals to try and get up with the first-team and get something after their two years with me.
"If one or two players every year could get something with the first-team, that's the level I want to get to, where every year there's always at least one player that's getting a contract with the first-team because they're good enough.
"But that also comes down to me as well, how much are we doing with these lads over two years to help them develop, which is where video analysis, Hudl, guidelines for success, individual reviews and position specific sessions all come in.
"If we've got a striker that's good at finishing, let's make him tremendous at finishing, if we've got a centre-half that's good at one v one defending or heading, let's make him the best he can be at that.
"Those are the things we pinpoint. If you've got a lad that's got a great trait, let's make it outstanding so when he goes into the first-team, the gaffer can go 'wow, he's brilliant at that one job he's supposed to do' and they can they mould and shape him for how they need him to be."