You and your employer broke the rules. The onus is mainly on the employer to operate PAYE correctly rather than on the employee.
The Revenue are generally willing to co-operate with somebody who is trying to fix things up provided that there is a willingness to pay the tax due -- and is seems clear that you want that to be done. I suggest that your employer phone the tax office, explain the "misunderstanding", and ask for assistance in regularising the situation. It might be tidier if your employer has not yet submitted a P35 (end of year PAYE summary for the business).