Your wife should complete and give to her employer a PA Rev 419 to stop all PA withholding ASAP..
http://www.revenue.pa.gov/FormsandPublications/FormsforBusinesses/Documents/Employer%20Withholding/r...
It's unclear if you were married in 2016 (that would be the return that is past due now) or if your talking about 2017. I'm assuming you are asking about 2016.
I would advise for each of you to file married filing separate for 2016 for both PA and WV.
For you, report all income on your WV resident return.
For your wife, she will need to file two part year returns (married filing separate).
All income earned by your wife while a PA resident is reported on her MFS part-year PA return. Include all PA withholding for 2016. If they withheld PA taxes the entire year, she should be getting a nice refund depending on her other income.
All income earned by your wife while a WV resident is reported on her MFS part-year WV return. If there was no WV withholding, she likely will owe taxes and possibly a penalty.
For 2017, if PA income taxes have been withheld, you would be eligible for a full refund of those taxes as PA does not tax the wages of a reciprocal state resident. File WV MFJ.
If you were married in 2017, then file the REV419 ASAP and file the separate returns for 2017. You may wish to file WV estimated taxes for 2017 but definitely will need to file WV estimates for 2018 to avoid penalties.
