I am not a city resident and I accidentally clicked that I am so now its saying I owe city taxes. How do I fix this?

After you file

Start the State return over again and you will get the questions again in the beginning.

After you file

Does it matter if I already got my refunds back? It won't affect that will it? Thank you for answering

After you file

Yes, it matters as you will need to do an Amended State return then to change the City taxes.
<a rel="nofollow" target="_blank" href="https://ttlc.intuit.com/questions/1894381-how-to-amend-change-or-correct-a-return-you-already-filed"...>

After you file

Also do I just choose amend as the option?