When I accept a deposit on an invoice. The full amount of sales tax is added into what I pay to CRA prior to doing the work and receiving full payment.

Hello hbpierce,

It's good to hear from you again. I hope all is well on your end and that you're enjoying QuickBooks. I'll be happy to share more information about accepting deposits on an invoice so you can record your transactions with peace of mind. 

To make sure we're both on the same page, could you elaborate more on what you'd to accomplish in QuickBooks? In the meantime, I encourage you to check out this helpful article that shows you How to link a deposit to an invoice. Feel free to get back to me in the comments below. You're more than welcome to attach screenshots for visual reference. I'm here to help you achieve your QuickBooks goals.