My common law partner and I currently live at both addresses of a duplex we own, and are self-employed working at home. How should I account for this?

You will both claim self-employed- working from home expenses. 

The Canada Revenue Agency (CRA) allows Taxpayers to deduct business-use-of-home (self-employed) or workspace-in-the-home (employee) expenses from your income which lower the amount of taxable income being claimed, which reduces the overall tax burden.

Here are the tax deductions you may be entitled to claim.