I live in Québec but work in Ontario. How does the program account for this? What do I need to do to make sure this is taken into account in my tax report?

You simply need to enter Quebec as your province of residence on December 31st, and when you enter your T4 slips, if the province is Ontario, you will need to choose the province of Ontario. If you do not have a Relevé 1 slip from Quebec, you simply skip it.  

You can transfer to the Province of Quebec up to 45% of the income tax shown on information slips issued to you by payers outside Quebec. In the provincial section under Other Quebec Credits, check the box that says "Tax transfer for residents of Québec who earned income in another province and from which federal tax was deducted".

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