For a married couple to file separately, is the most costly way to file tax-wise. When a married couple files separately they both "automatically" disqualify themselves for a number of deductions and credits they qualify for if filing joint.
So when filing a joint return, it's not "my" tax return. It's "our" tax return. You must include all income from all sources for both of you on that one tax return.
When you start the tax return you begin with the "my info" section. Work through that section again in it's entirety and make sure you indicate you are married and that you *DO* want to file a joint tax return. Then when you get to the income section it will ask for the income for each of you, one of you at a time.