How can I mark a transaction with an "R" in the check box if there is no check box visible?

The trouble ends here. I'd be happy to help your mark the entry as reconciled in QuickBooks Online (QBO).

To start, could you tell me what specific type of transaction you've entered and want to mark as reconciled? That information is a great help so I can provide an accurate solution. 

In the meantime, you can follow the steps below to help you reconcile the transaction.

Let's start with making sure that the entry is posted to the correct bank or credit card account in your QBO. Once verified, you can now manually reconcile it from there. Here's how:

1. Select the Gear icon and choose Chart of Accounts. 
2. Next, find the bank or credit card account where the transaction is allocated and select the View register option.
3. Click the small Gear icon and make sure that the Reconcile and Banking status box is checked. 
4. Select the Gear icon again to close the small window.
5. Once done, find the entry you need to mark as reconciled. 
6. Select the space under the Check sign row and continuously click it until you see the R sign.
7. To save the changes, select Save.

For more information about the process, feel free to read this article: Undo or remove transactions from reconciliations in QuickBooks Online.

The program also creates a report after every reconciliation you've performed. You can use this as a guide to avoiding mistakes in your future reconciliations. To get one, check out this link: How do I view, print, or export a reconciliation report?.

If you have any other concerns reconciling your account in QBO, please don't hesitate to leave a reply below. Have a good one and stay safe.