When the QuickBooks integration is first enabled a default bank account is selected to create Bank Deposits in QuickBooks Online. This is fine temporarily, but it won't allow those Bank Deposits to match with the deposits that are being reported by your bank.
Note: Transfers are sent to the bank account you have configured in your Company Info settings.
To adjust this, go to your Integrations Tab and select the bank account that matches the one configured in your Company Info settings.
This will ensure that your Transfers are being fed into the correct account and you'll see the "Match" option in QuickBooks when the deposits are reported by your bank.
What this also means is that in your Chart of Accounts
You'll have an account called 'Goodshuffle Transfers'
You can then quickly access these Transfers and click 'Edit'
Finally, you can select the correct account for this Transfer.