The allocation can be done entirely in TurboTax. Likely, however, all of the wages for that NY job are NY source income. Here is a link for reference.
In short, if a non-resident taxpayer is assigned to an office in NY and works in NY and at home out of NY due to a necessity of the employer, then those days are all typically NY workdays. However, if the home outside of NY has been established as a bona fide office of the employer outside of NY, then days worked at home are non-NY work days. (See pages 2-5 here for the definition of a bona fide office).
Based on her W2, the employer considered all the days worked for the company as NY days and taxable by NY. She'll file a non-resident NY return and allocate all the wages reported on that W2 to NY. She should work that state return first and note the income taxed and NY tax liability. TurboTax will use those numbers to claim a credit on her resident NJ return.
If the home days are indeed non-NY work days, then in the NY return in the allocation interview, she will have the option to allocate by workdays. She'll follow the prompts to enter the number of working days, number of NY working days, and number of non-working days. There are helpful links imbedded to assist with the definition of each category.
Her resident state, NJ, taxes all income no matter where it is earned therefore there is double taxed income. To mitigate that double taxation, NJ offers a credit for taxed paid to another state. By working the non-resident return first TurboTax will transfer the numbers needed to the NJ return for that credit. She'll find those interview questions in the credit section of the NJ interview.
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