When my customer takes longer than allowed, the comptroller pays me interest. How do I document that? If I receive the higher amount it shows as a credit to customer.

Welcome to the Community, @employmentconsul. 

I'm here to help you ensure you can record an interest in QuickBooks Online.

Since the comptroller pays you the interest, you can set up first an Income account. I'll show you how to do it: 

1. Go to the Gear, then select Chart of Accounts.
2. Hit New. 
3. Under the Account Type column, select Other Income. 
4. In the Detailed Type drop-down, choose Interest Earned. 
5. Type a specific name in the box. 
6. Tap Save and close. 

Once done, done, receive the payment to document the interest. Then, create a Bank deposit as a positive amount. Here's how:

1. Tick the +New icon and choose Receive Payments.
2. Enter the payment information and put a checkmark next to the invoice you like the payment to be applied.
3. Choose Undeposited funds as the deposit to account and click Save.
4. After that, click +New, then choose Bank Deposit.
5. You should see the payment you entered in the Select Existing Payments section at the top.
6. Place a checkmark to select the payment you want to deposit.
7. From the Add other funds to this deposit section, enter the amount as a positive amount.
8. From the Account ▼ dropdown, choose the Expense account you want to put the money into.
9. Verify that the deposit amount is correct and click Save.

For more details, check out this article: Record and make bank deposits in QuickBooks Online.

For future reference, you can also check out these resources here to help you organize your accounts in QBO:

• Learn the reconcile workflow in QuickBooks
• Reconcile an account in QuickBooks Online

If you need further assistance in recording your transactions, you can always drop a comment below. I'm here to help you in any way I can.