For the current FAFSA, you use the parent with whom you lived the most day from the day of filling (say you do it today, Oct 17) back one year. So who did you live with the most overnights from Oct 18, 2020 to Oct 17, 2021 ?
If you use your mother’s income, she will have to apply for a FSA ID (as will you) and then fill out the information. Since she didn’t file taxes in 2021 for 2020 earnings she won’t be able to use the tax DRT to transfer info, so will probably be required to give a 'non-filer’s statement to schools. She should order one of these now as they can take a while to receive.