Since you are a nonresident for California, you would be correct in filing your amended returns using the 540NR and including Schedule X, California Explanation of Amended Return Changes for the applicable years.
As far as which program to use, you can either use the tax forms from the CA FTB website or download the prior year TurboTax software using the instructions in this link. Please note you must amend your returns within three years of your original return or within 2 years after you paid the tax due on your return (whichever is later).
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