O’Neill has been in charge at the bet365 Stadium since November, replacing sacked Nathan Jones, and has led the Potters up the Championship table.
They are currently in 17th place in the table – three points above the relegation zone.
“We have a lot of people at the club who have spent a long time in the Premier League but the priority now is to make sure we don’t end up in League One,” O’Neill said, speaking to the Daily Mail.
“When clubs have four managers in two years you get a fractured squad. There was a lack of balance here.
“There were a lot of disillusioned players too and we simply had too many bodies. And when we got to games, a lot were left out of the squad and that leads to disharmony.
“We streamlined that in January. A lot went out and a different type of player came in. Now we have some harmony.”