It is possible for your federal return to be rejected by the IRS, and your state return to be accepted. In fact I had that happen yesterday with a Georgia return. If that turns out to be the case, then your payment would be drafted by New Jersey even if you pay online. I would wait and see if your New Jersey return is accepted, and if it is, you've got nothing to worry about. If it is rejected, then file by mail and pay by check or online. Include a statement with your return as to why the payment is late. If they assess a penalty for late payment, appeal it.
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