Yes, your wife has file her tax return if you filed your Illinois tax return as Married Filing Jointly.
If you filed as Married Filing Separately, she has not filed an Illinois tax return.
When you enter your own information in My Info, you have to answer the question "Were you married?" If you click the button for Married, then a drop down will appear that asks, "Do you want to file this return together with your spouse?" Then you choose yes to file a joint return. You would then enter your spouse's information into Personal Info. Whenever you are entering income information there should then be a spot for you and for your spouse's income information.
When you prepare a joint return you include all the information for both spouses on the SAME tax return. Include all of your personal information, all of your income from every source, all dependents (if any), all credits and deductions for both of you. You get ONE refund with both names on it.