If you go to "Receipts" then "create receipt" in the receivables window, there is an option to enter a customer deposit. This will then be recorded in a liability customer deposit account. You can also print a receipt for the customer. 

Thanks for the tip! Will this work if I need the taxes to be in my GST/QST return?

I believe that as this is a liability (money for work not yet completed) and you have not yet recognised the revenue, taxes are not charged on a deposit. When the work has been completed and you are invoicing the customer, revenue would be recognised at this point, so taxes would be included on that invoice. Even if the amount due was $0, because the customer had prepaid the full amount, you would still produce an invoice with the subtotal and GST for the work done, and then subtract the amount of the deposit paid. So at this point, the amount of taxes collected would be recorded. Hope this makes sense!

This is exactly what I was doing until my accountant told me I have to charge taxes on deposits because something like there is a contract with the client and the deposit is a part of the work in progress starting on the signing day (Unlike a product).

Is this more-or-less the situation?

https://sagecity.na.sage.com/ca/sage_50_accounting_ca/b/sage_50_ca_supporthub_blog/posts/how-use-contract-for-progress-billings-in-construction-industry