You need to enter them as just one W-2. Just add the boxes with the city tax onto the other W-2.
If one of your W-2s is mostly blank, just enter the other W-2 and make sure you include the info from the mostly-blank W-2. Usually, "blank" W-2s have additional Box 12 line items or entries for a second state in Boxes 15-20.
Don't enter a separate W-2 if Box 1 is empty, as you won't be able to e-file.
