When you go to Auto-Fill you will see your name on the top, therefore, you will be auto-filling your information- If you go back to Auto-Fill once you have completed yours then you will continue and it will ask if you'd like to Auto-Fill your spouses, it will have her name on the top and she will need to sign into her  CRA "My Account". 

I have a similar issue (I created my own thread)  . Going back to Autofill keep asking only my CRA account and it never ask for spouse, I am stuck and don't know what to do as I need to file it with my spouse. You can check detail in my thread.  Thanks

If you have already Auto-Filled your return- and you went back it will ask you again to Auto-Fill you will click on "SKIP". The next step should then look the same, but have the name of the other spouse on it. This is the step to Auto-Fill for that person.

When you create a return it asks if you want to process your and your spouse's at the same time. If you do that on each page there's a little yellow marker at the bottom in a checkbox to say whose return it's for. Check your wife's box, then in the File menu top left select "Import tax data from CRA"