I had used my wife's ITIN as the IRS did not figure out her SSN that she got after she started using ITIN. Now she has income with her SSN. Which number have I to use?

In her basic information, I put her ITIN but had to use her SSN in her income section as her W-2 form has her SSN information. So have I to keep these two numbers (ITIN in the basic information section and SSN in the income section) or use her SSN even in the basic information section?