If you use the Transaction Report from the reports repository there is a column for sales tax, and also a column for Marketplace Withheld tax. The withheld tax is collected and remitted by Amazon to the appropriate authorities, as 'Amazon.ca' or other relevant entity. Not as a seller, or on behalf of any sellers.

So I hope I am correct in saying that when filling out your t2125 (or other self employment/business income from), in the line for "gross sales (including sales taxes)", you would actually input "gross sales(including sales taxes, except taxes collected/remitted by Amazon)".

You can find out the amount to add to your gross sales by Subtracting the 'Marketplace withheld Taxes" from "sales tax"

I would put links supporting this, but for some reason I can input links to amazon seller central help or FAQ's. We should get this fixed.

Note: keep in mind any text above with in quotations (",') may be worded differently for you.