How to apply a single payment to multiple companies

We can set up a clearing account, HeatherL21.

This is use to transfer funds from one account to another. This to ensure that the movement of the money is properly tracked. Here's how to create a clearing account:

1. From the Lists menu, select Chart of Accounts.
2. Click New on the Account drop-down.
3. Select Bank as the account type. Click Continue.
4. You can enter Barter Account or Clearing Account as the Account Name.
5. Hit Save & Close.

Once done, let's deposit the payment worth $1000 you've received.

1. Go to Banking and select Make Deposits.
2. Check the payment on the Payments to Deposit window. Click OK.
3. Select the correct Deposit To account. 
4. Add a -200 on the second line. Hit Save & Close.

Also, we'll have to create a Check to offset the $200 on your Barter account.

1. Click Write Check on the Banking menu.
2. Select the Barter account on the Bank Account drop-down.
3. Go to Expenses tab and select Accounts Receivable.
4. Enter 200 as the check amount.
5. Under the Customer:Job drop-down, select the affected customer. 
6. Hit Save & Close.

Then, let's receive a payment again to zero out the $200 credit.

1. Select Receive Payments on the Customers drop-down.
2. Choose the affected customer. You'll see a pending $200 transaction.
3. Click on Discounts And Credits. Select the available $200 credits.
4. Hit Done. Click Save & Close.

To make sure everything's good, run the Open Balance report for the affected customer. Select and right-click on the customer, then click Open Balance. It should be zero. The Barter account should also be zero balance.

In addition, we also have to create a new Barter account on your second company. Then, make a deposit worth $200 to record the money in. Use it and apply as a payment on the pending invoice.

We're now done! These steps will help you to record the payments properly. Comment again if you need additional assistance.

When I receive payment of the $200 it shows up as a payment in the Payments to Deposit window.  What do I do from here?  I don't want to deposit it right?

Hello there, @HeatherL21.

Let me provide more information on how to apply for customer payments in QuickBooks Desktop.

If you're using QuickBooks Payments when processing ACH payments, you have the option to link it to your company file. This way you can send invoices that will be deposited directly into your bank account. Here's how:

1. Click the Customers menu.
2. Select Link Payment Service to Company File.
3. Enter your User ID and Password and select Link Service.
4. Hit Transfer then Yes, transfer.

However, if you're using a different service, you can manually receive your customer payments. You can deposit them in the Undeposited Funds account to hold the funds until you're ready to deposit them. I've provided the steps below:

1. Click the Customers tab, then Receive Payments.
2. Enter the customer name in the Received From drop-down.
3. In the Payment Amount field, enter the payment you received from the customer.
4. Press the More button, then Add New Payment Method button.
5. Set up your payment method then click OK.
6. Mark the invoices you want to receive the payment.
7. Hit Save & Close.

If you have further questions, we're just right here to help you.