But, Zullo added, the most important thing was that City had multiple formations it could switch to with confidence going into or during games in the crucial 10 rounds that are left before the finals.
City will attempt to bounce back from their 4-3 away loss to Wanderers when they meet a desperate Newcastle Jets outfit in the round-18 clash at Hunter Stadium.
"To be able to play more than one formation is a pretty valuable asset to have," Zullo said.
"If one formation isn't working we've got the confidence to go back to the other formation, which we've done at times (during games) in the last couple of weeks as well and it's had a pretty positive effect on our performance.
"I think it would be premature just to throw out the 3-5-2 at this stage, because there have been some pretty positive signs. It's just about perfecting it."
Zullo said the players had embraced playing with a back three, but because it wasn't easy to play they were still working on getting it right.
"I think it's a massive change from everything people are used to," he said. "They're used to the 4-3-3 or 4-4-2, and 3-5-2 is a massive difference in terms of build-up of play and transition and I just think it takes a bit of time to get used to it.
"We definitely still haven't perfected it, but each week we make little changes to see if that works and we keep trying to adapt. It can definitely be something we can use to our advantage because we have very good players in all the key positions who are very adaptable.
"We have the players to make the formation work, but it's a pretty hard slog for a lot of players on the field and at the moment it's not working exactly as we want it to be but I think we're heading in the right direction."
Zullo said it was up to coach John van't Schip to decide whether to continue to start with the 3-5-2 in the coming weeks.
"It's in the coach's hands and it depends on the opposition and how we're going, but I think we've shown in patches it can be a very good formation for us," he said.
"First time we used it was against Sydney FC at home (in round 13) and it went pretty well, changed the game to be honest, and also against Wellington it went really well, but against Wanderers they obviously analysed our game really closely and found some areas where they could exploit us.
"They worked out how they could infiltrate our defence, I guess. We had some strong possessions throughout the match, but as soon as we lost the ball it was pretty obvious what their tactics were and that was to exploit the areas myself and (fellow wing-back) Ivan Franjic had vacated.
"But there are ways around that, to fix that with a few tweaks. It forced us to have another look at it and think of where we can improve, which we've done, and hopefully that will pay dividends.
"For me, it's about learning a new position as well which is a fair bit different to regular left back or left wing. It's kind of a fusion of the positions I'm used to playing in my career and I'm really enjoying it to be honest.
"For the team as a whole, it's about us being flexible and being able to use different formations.
"It's a massive game for Newcastle on Sunday, but it's a massive game for us as well. It's important we bounce back positively after a loss."
