I am a Canadian company, but most of my customers and income is in USD. What to do in new QuickBooks Online?

If you are using the Canadian version of QBO you should have HST and multiple currency feature available. It is not available in the US version of QBO.

You will need to set up or edit a customer, on the payment info tab, you indicate US currency.

When you enter transactions, QBO will create entry for currency gain or loss.