I live in NJ and work in NY. I am only being taxed in NY. Do i remove the NY jurisdictions from the Nj section, as i was only taxed in NY and not in NJ.

No, you will need to file both a NY Non-Resident Return and a NJ resident return.  Since all of your income is earned in NY, you will report ALL of your income on both your NJ and NY returns.  You will file your NY return first and then take a credit on your NJ return for taxes paid to NY. 

 You may or may not still end up owing money to your resident state depending on whether or not their tax rate is higher or lower than your nonresident state.  If the non resident state had a higher tax rate than your resident state, your credit will be limited to the amount of tax you would have paid to your resident state.  They will not give you a refund of the taxes you paid to the nonresident state. 

Multiple States

File Non Resident State Return