How you listed your status on the W-4 you gave to the employer for tax withholding has no relevance when filing your tax return.
Since you are legally married you should be filing as Married Filing Jointly. On the tax return use the name that is on your current Social Security cards.
Enter each W-2 separately for each of you. After competing one W-2 the program will ask if you have anothter W-3 to enter. Make sure you indicate who the W-2 belongs to when entering the W-2.
