Amazon offers many services and programs to sellers, and fee taxability varies based on a combination of the type of services purchased, the Amazon entity providing the services, federal and provincial tax laws, your participation in Tax Calculation Service (TCS), business information you supply to Amazon, including your federal/provincial registration number, the location of your business or where an FBA service is performed.
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You can read all about Canadian sale tax on Amazon fees in this help article from Amazon.

The charts below illustrate when an Amazon.ca seller fee may be subject to sales tax in various Canadian jurisdictions.

We don't currently have a way to split fees out by fulfilment centre location unfortunately so we suggest as a workaround that you set GST/HST on Purchases as the tax rate for all Amazon Fees (Seller Fees, FBA Fees, Storage Fees and Advertising Costs) in Link My Books and then once a month use the tax invoices from Amazon to adjust for the taxes accordingly directly inside Xero.

To adjust for your Canadian PST/QST on fees follow these steps:

You would effectively make a journal entry crediting the total amount of fees from the relevant fees account with your GST/HST on Purchases tax rate and then replacing them with the correct PST/QST tax rates.
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If we take an example of a business established in Ontario.

Here is an example of what the tax summary section would look like on one of their Amazon tax invoices:

Note that only the BRITISH COLUMBIA and QUEBEC locations are having Provincial Tax applied.

So we need to adjust the tax rates on those fees only.

In Xero, the journal entry would look something like this:
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What we have done is:
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-$15.00 FBA fees with ON - HST on Purchases

+$0.06 FBA fees with BC - GST/PST on Purchases

+$14.94 FBA fees with QC - GST/QST on Purchases
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Meaning the total FBA Fees is the same as before but now the correct tax rates have been applied.