When New York requires total Federal wages to be reported in Box 16. how do you file the state as its considering total federal for both CA and NY?

[DanielV01]

For New York you must utilize the allocation screens to report the income earned in New York.  There are several acceptable methods to determine the taxable NY income.  If you know the exact amount, then use that amount.  If unsure, New York will allow you to use the method of percentage of working days.  (They have a form, IT-203-b, that handles the calculation).  The basic idea is to divide the number of NY working days by the number of working days everywhere (not 365 calendar days, but the actual number of working days), and then multiply your income by this percentage to determine NY income.  

The reason why NY requires this is because they do not allow the companies to assume that your income is not NY-sourced income.  For example, NY requires a telecommuter working from home for a NY company to pay NY nonresident tax on income for a company operating out of NY, and they aggressively enforce this law.  

If you live in CA, California will tax all of your income, but will also allow you to claim a credit for the tax you pay to NY on your income earned there.