QB Issue Resolution:

If your bank is connected to your QuickBooks Online account, you can create the transaction and “Add fund to this deposit” and select Bank Charges from the drop down box, then enter the amount as negative ($-2.16). By doing this, when we look at the transactions, the amount of the invoice and the payment are the same, so the customer’s Account Receivable will show that this invoice was paid and the bank account will show the deposit.

 

See screenshot below.

 

That’s it! This will get everything nice and organized in your QBO account once again.

Resolution for Issue 'I have four payments in two separate online deposits. I can see the deposits on the list, but they do not show on the account when I reconcile. They do show on the paper bank statement so I do know they where deposited, how can I make these appear?' available: Yes (Solved).
Source: Intuit Community forum.

I have four payments in two separate online deposits. I can see the deposits on the list, but they do not show on the account when I reconcile. They do show on the paper bank statement so I do know they where deposited, how can I make these appear?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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