If boxes 1-6 are different on each form, treat them as two separate W2 forms.  If you add the two box 1 amounts up, this should be very close to what was originally reported to you on your final pay stubs.  

It happens from time to time, for example, that a company may change its payroll company.  When they do, two separate Forms W2 get issued from each payroll processor.  This may also have been the case for working in two separate states, and your employer/payroller decided to report it this way.  Either way, enter them separately because the two amounts should combine to reach your final wage total.