You can do it either way as long as you end up apportioning the income you earned while in NY as NY sourced income. The bonus does not need to be allocated to NY, so you can subtract it out and then allocate based on days. If you have figured out the amount that should be allocated to NY, you can enter that amount as NY income and then choose ''don't allocate this employer''. CA is going to tax all of it and then issue you a credit for the taxes you pay to NY. This will ensure you are not double-taxed on any of the income. But you only need to include the income from the days you were in NY on the NY return.
Do I need to file a nonresident return for an out-of-state employer?
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