Enter the CA and the NY information as it appears on your W2, and all as if it was just one W2 (because it is). Ignore the general all states information and don't enter it.
The New York return requires you to use allocation screens for you to claim your New York income. You can use the percentage method. Subtract California income from total income, and divide the result by total income. Enter the percentage without the symbol (.0833 would be 83.33) This will give you the correct New York income, and it will calculate from there.
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