Sales taxes not reporting properly

I have taken over bookkeeping in Quickbooks Online for a small restaurant/pub in BC Canada that also sells merch (t-shirts) and does cabin rentals. They use Touchbistro to enter sales of food, beverages and merch, and Campspot for the cabin rentals. There are two different merchant accounts collecting and depositing money daily to the bank account.  All revenues are directed to the Cash Clearing account which is cleared at the end of the month with a journal entry to separate the revenues into different categories, and to record the sales taxes collected.

In BC there are 3 PST tax rates: 7% on meals and non-alcoholic drinks, 10% on alcoholic beverages, and 8% hotel tax on the cabin rentals.  There is also the 5% GST on everything.

When money is deposited from the Merchant account, I can't enter all of the individual tax rates on the single deposit, which is why it is broken down in one journal entry at the end of the month.  However, when done this way, when you do a GST/HST Summary Report, because you didn't enter a tax code on the deposit, no revenue or taxes are recorded on this report, only the GST ITC's (input tax credits from purchases).  

Is there a better way to do this so the tax reports will work properly?