Clearing account for 2 party check and more

Set up  a (clearing) Account.
1. Go to Lists>Chart of Accounts and right click on any account
2. Choose New and choose Bank for the type
3. You can name it whatever makes sense to you such as Clearing Bank Account
4. Use this account to post to for both transactions, Income and Expense and they will zero out the account and no Income or Expense will be realized.

Enter the full amount of the Customer Payment in Receive payments if tracking Customer payments.

When you make the deposit use the Clearing account to "deposit" to.

If paying a Vendor or using an account such as Paypal that you need to track you can enter a "check" or pay a bill as you normally would EXCEPT you will pay with the Clearing Account.

The Customer Invoice will show as paid, the bill will be paid and the clearing account balance will be zero.

or

When you go to deposit the Customer payment, enter a 2nd line using the Vendor name and Accounts payable in the from account and enter a negative amount.
Then go to Vendor>Pay bills>choose the bill and click the set credits button.