There are specific "forms" provided in accounting software for each type of transaction.  If transactions are recorded by General Journal Entries instead of using the correct forms it is highly likely that many of your reports will be incorrect.  Sales transactions, for example, should be recorded by Invoices or Sales Receipts as impossible said. 

The only way to obtain a correct value on Line 101 of sales tax reports is to delete all your incorrectly-recorded transactions and re-enter them correctly.  Alternatively, for THIS GST return, obtain the correct amounts for each line of the return from other reports (P&L, QuickReports, etc.) and file your return by NETFILE or paper.

Going forward, try to enter transactions correctly so that you may have the option of filing electronically.  Consider consulting a QB ProAdvisor in your area for training.