The other replies don't make sense to me. I'm in your same boat. I owed $ to NYS. I did everything online, on time (in April). Paying online, was auto-offered use one of their convenient apps. Of the diff options, I chose Pay1040. 4-5 months later, NY State mails me, asking where their money is. What?!! Turns out Pay1040 is ONLY for Federal - not State. NYS phone rep said past due fees would begin to incur, and I could write Fed Gov to refund ME the $500+ I'd paid them by mistake (since it 'wasn't their problem I paid the wrong entity). So no - you won't be "fine". You may start to incur interest fees due on what they consider your 'late payment'. Check into it.
