Yes, you will enter both as dependents. However, the tax credit for an eligible dependant can only be claimed for one child. Type your son's net income (0) and uncheck the box where they asked about his earnings in the year.

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If we have two kids that we share custody, can she select one child and I select the second child? 

@imabou A parent may claim their children as dependents if they live with them. One common misconception is that both parents can claim the Eligible Dependent Tax Credit in a shared parenting situation. However, only one parent can claim the credit per tax year

Refer to the CRA article for more information. Child custody and the amount for an eligible dependant

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