State tax filing

@Vanessa A  this may be a dumb question but when I file the PA return is the New York non resident returned filed together or will those be two separate filings?

How would this work if I am married filing jointly (husband works in PA and company is in PA)? Also the last part about having to owe PA depending on my tax situation is there a way to prepare for that ahead of time. Like designate extra Federal withholding to be taken out of every pay?