What is going to happen is as follows, the NY and Va taxes withheld which was originally reported on your federal will automatically flow through to these two state returns. There is no need to allocate those. However, as you go along the input for filling out the actual state returns themselves, you will be led to screens that will ask you to allocate the wages. So, for the bonus and stock which most likely got reported on a W2, you will allocate 2 months worth (approximately 17%) to Va and 83% to NY.
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