Let's get everything recorded so you can reconcile your account, userhpdpco.
We'll have to record the GST expense that directly reflected in your bank statement to your QuickBooks Online. With this, you should be able to reconcile the account. You can create an Expense or Check to record it:
Make you refer to your bank statement when reconcile an account QuickBooks Online. Here's a link for the step by step process on how to do it: Reconcile an account in QuickBooks Online.
You can always get back to us if you have additional queries in recording your transactions or reconciling your account.
You will have to create a Bank as vendor for these charges and book bill of bank charges and transfer the amount deducted basic + tax to this bank vendor account. By doing this you can get the same in ITC report and also while reconciling the same with 2A you can get the mapped to GST of the bank.
Do let me know if you have issues.
CA Alok Shah