Income taxes for independent contractors

So, I am helping to prepare federal and state income taxes for my daughter. She worked as a w-2 employee for 2 months and then changed jobs and became an independent contractor for the rest of the year. She lives in Minnesota but works remotely and her entire income is from a firm in Virginia. She paid estimated federal taxes but forgot to do state. Does she pay state taxes to Minnesota (resident state) or Virginia? Does she have to file for both states although paying taxes in only one state. Also, are SEP IRA contributions for herself reported as a business expense on schedule c or a reported on schedule 1.

I have researched both items and have a good idea but wanted a cross check since this is her first year.