HST Amended Returns

I have just started here and the person previous to me completed the Q3 and Q4 2016 HST returns incorrectly.  We owed more in both quarters.

HST returns were amended and manual cheques were written for Q3 and Q4 2016 this month (April 2017).  I know have to do a general journal entry for these two cheques, I debit HST on sales and then credit the bank account correct? 

I have not completed the Q1 2017 HST return yet, if the amended ones were not corrected until April 2017 will this affect Q1 2017 HST return?

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    Depending when your year end is. If it is December 31st and that year has been closed you will have to do your entry into 2017. Because HST and/or GST are running balances in the GL you would do the entry that you mentioned to clear it. If the error was caught in the Year End Process, your accountants may have set up the amount owing in Accrued Accounts Payable. If they didn't do that then do your entry and normal.