Hi, I have a question,

My wife works in ny but lives in nj does she have to pay taxes each week to both states. Currently her job is only taking taxes for nj... Any help with this would be great, taxes and answers to this is very confusing. Thank you in advance...

She should be having taxes withheld for NY, not NJ. The reason is that as a non-resident worker the state of NY will tax her earnings, and NJ will also try and tax her earnings, but will give a credit for taxes paid to NY. Since NJ's rates are lower than NY's, in the end she will most likely owe no taxes to NJ for her wages earned in NY. So she should talk to her payroll department to change the withholding so that it goes to NY, not NJ.

If you earned income while in NY, you must report this on NY tax return. You will file nonresident tax return if you did not live in NY.
As a NJ resident, you will report all your income on NJ tax return. You will also claim credit for the taxes paid to NY.