Two customers paid for the same invoice.

Checks get posted to the company they came from.  Company that has the invoice will match to the invoice. 

Company that sent the extra payment should show a Credit.  And I would recommend you DO NOT apply the check directly to any invoices that company may have outstanding.  It will get VERY confusing if there are other issues down the road.  Be sure to issue them a Credit.

Then when you are apologizing for the error, you can find out if they want to apply the check to another invoice, keep it as a credit on their account for the next invoice(s) or if they want you to send them a check for the amount.  Regardless of their answer, working with a Credit will be much easier.

Hey there, gacosta. Welcome to the Community.
 

There's a few options to enter deposit records in QuickBooks Online. You can use our Bank Feeds feature, upload the data from your bank, or enter them yourself.
 

Here's how to manually input a banking record:
1. Use the + New button, then pick Bank Deposit.2. Choose an account you want to enter data under by using the Account drop-down menu.
3. Tick the box for which payment you'd like to combine and confirm your total matches with it's corresponding deposit slip.
4. Select Save and close.

To give your customer a credit, you can create a memo and apply it to their profile:
1. Click + New.
2. Choose Credit memo.
3. Input the customer's name.4. Enter the appropriate information in your required fields.
5. Hit Save and close.

Now your customer will have an available credit which can be applied to their open invoices. This process can be done manually or automatically. If you'd prefer to return your customer's money, you can issue a refund.
 

I've included a link to our resource archives for QBO, which might come in handy moving forward: Help articles
 

Please don't hesitate sending a reply if there's any other questions. I'll be here to assist. Have a fantastic day!