<p>It has been a while since I had to file a NY non-resident form but in the past the form had one column for total income that had to match the federal return and a second column where you listed the NY based income. If I remember right, NY would tax the total income as NY income and then multiply the tax owed by (NY income)/(total income). The resident return should ask if you paid taxes to another state and make an adjustment. I have no idea if California has that adjustment.</p>