Hi there, Lisa-S.
Thanks for joining the Community. I'm here to address your concern with depositing customer's payments in QuickBooks Online (QBO).
Yes, you're doing the right process. You can create a bank deposit that includes a negative value. To do so, please follow these steps:
- Click on the Plus (+) icon.
- Select Bank Deposit.
- Choose an account.
- Mark to select the $5,000 payment.
- In the Add funds to this deposit section, select a customer and expense account. Then, enter a negative value (-$250.00).
- Click on Save and close
For your visual reference, you can also check out this helpful article: Record Bank Deposits in QBO.
This should point you in the right direction. Leave a comment below if you have further questions. I'm always glad to help. Have a great day.