Thank you JaeAnn - I contacted online support and they explained that the State filing was still pending approval (I'm not sure if it is approval for our specific company or for Quickbooks Online to file in my state for any business), however they said that we should get an email in about 4 weeks to confirm if it is active, and that in the mean time just to pay manually.
Nothing on Quickbooks Online explains this, so you really need to contact an agent to find this out, which isn't ideal.
