To handle GST correctly, you must file the GST Return in Quickbooks. I always file the Return in QB first, then file the Actual Return with the CRA to match. Since you are behind by an entire year, each quarter must be filed in QB sequentially. Here's how:
Click Sales Tax on the top icon bar and select File Sales Tax
Select the Sales Tax Agency - Receiver General
Enter the Date Parameters (on the top RH side. In your case you will want to select the first Qtr for 2015 to begin with. If your Fiscal Year coincides with the calendar year the From Date would be Jan 1, 2015 and the To: date would March 31 2015.
If everything was recorded correctly, the bottom of the return should have green checkmark - Your Return is ready to file. Click the blue File Return tab
In the next screen, select the file Paper return option. Print a copy of the Return.
In the Next screen, select Pay Now. QB creates a bill and opens the Pay Bills window. select the Receiver General Bill, enter the amount of the Payment Cheque you wrote for the first Quarter (if different from what is displayed) and complete the payment details at the bottom (Chq Date, Payment Method -select cheque>assign chq #, and the Bank it was drawn on. Click Pay Selected Bills. In the next screen enter the cheque Number and click Done.
If there was a remaining balance payable (or a Credit Balance) always pay (or apply the credit) the previous balance first - before making the payment towards the next quarter.
Follow the above steps for the next three quarters - one quarter at a time.
When you have filed the last return and recorded the last remittance Cheque, it is entirely possible that there will be an outstanding amount. Since Sales Tax is cumulative and there are already transactions recorded in the current year, it is unlikely that there will ever be a zero starting balance.
Above is the most accurate way to accomplish what you need. The Quickest would be:
File only a single Return in QB for the entire year (2015), selecting Jan 1, 2015 as the from date and Dec. 31, 2015 as the To date. QB will create a Bill for the entire year. In the Pay Bills Screen, apply the Payment Cheques one at a time to the Receiver General Bill.
If there is a Balance outstanding you will have to include with your first 2016 Remittance. Or, if there is a Credit Balance, you will reduce your first 2016 Remittance.