I can't seem to get the check numbers to show up in reconciliation, even when I select "reference number" in the column settings.

Welcome to the Community, martinson-laura.

I can help you through on how to see the check number when reconciling. 

To view the check numbers on the Reconcile window, you can add the Reference number column. To do this:
 

1. At the top menu, click the Gear icon.
2. Select Reconcile.
3. From the Account drop-down menu, select the appropriate bank account.
4. Click Start reconciling or Resume reconciling.
5. Enter the information requested.
6. Click Start reconciling.
7. On the Reconcile page, click the small Gear icon.
8. Under Edit columns, put a check in the Ref no. box.

I've attached an article and screenshot for additional reference: How to reconcile accounts.

By doing so, you'll see the check numbers on the reconcile page in just a few clicks.

You can always drop me a reply below if you have additional questions about reconciling in QuickBooks Online. Have a great day.

When I put in the invoices, 'bills,' to our company into quickbooks I use their reference number.  When we generate checks the check number is applied AFTER we've already put the bill in.  To reconcile with the bank I need the check number,  not necessarily the reference number I put in when entering the bill.   Ideally, we'd have both the reference number of the vendor's invoice AND our company's check number to reconcile with the bank.  How do I see both?

You can add the bill number as the reference number on the Bill Payment page and the check number as the memo, @Clark05. I'll walk you through the process.

After creating the bill, you can create and associate a check to make a payment.

Here's how to add a memo to the Bill Payment page:

1. Click the + New button and choose Check.
2. Choose the Payee name and add the necessary details of the check.
3. Select the bill on the right side to associate with the check by clicking Add.
   
4. Enter the check number in the Memo box.
5. Hit Save and close.

Start the reconciliation process and refer to this article for the detailed steps: Reconcile an account in QuickBooks Online.

If you want to correct your past reconciliation, here is an article you can read to help you fix the error: Fix issues for accounts you've reconciled in the past in QuickBooks Online.

We are committed to providing you with prompt and personalized responses to ensure you receive the best possible assistance. Comment below if you have questions about reconciling an account. I'm always here to help. Have a great day.