Hello there, KathyF.
I appreciate you for taking the time to reach us back and provide additional details of your concern. I'm here to make sure you're in the right track of handling this situation.
As I've read through the whole thread, I come up with this resolution. Since you've already created a Bill and an Invoice for your vendor/supplier, we'll just need to apply the payment from each of them.
Before we start, let's set up a clearing account or wash account to move funds from one account to another.
Now that we're done setting up a Clearing Account, let's create a Check for your Bill and apply the Clearing Account. Let me walk you through the steps below:
Once done, let's Pay Bills to link your Bill and Check. Below are the steps on how to do it:
For the Invoice created, we can create a Bank Deposit before Receive Payment.
To create a Bank Deposit, here's how:
Once done, let's Receive Payment to link the Deposit and Invoice. Doing all this should zero out the balance of your Clearing Account.
That's it. If there's anything I can further assist you with the whole process, please let me know. I'm always here to help you out.