If your job is the sole source of PA income and your employer correctly withheld NJ taxes since NJ and PA have a reciprocal agreement, then you should not have to file a PA tax return at all. You can verify which state withheld taxes on your W-2 by looking at Boxes 15-17. If that is the case, in the My info tab, under Other state income, you can answer No to earning income in another state. You can then delete your PA nonresident return.
If you are required to file a PA tax return, either because your employer withheld taxes in error or you have other sources of income that are PA sourced, like partnership income or a rental property, then only that PA sourced income should be taxed by PA. Any capital gains from stock trades should not be allocated to PA. If you only had your employment income because they withheld PA taxes in error, you should have $0 of PA income and receive a refund of the entire amount in Box 17 of your W-2.
If your employer is withholding PA taxes, you will want to notify the payroll department to start withholding NJ taxes instead. It will save you a lot of trouble at tax time.
