Hello there, WearHaus.
You'll have to make sure that the "From Account" used when you created the Deposit, is the Accounts Payable account.
Once done, let's review the vendor Credit created. Use expense account used from your original Bill. Which is you are choosing the correct account, based from the screenshot you provided.
We can now link the deposit to the Bill Credit.
- From the Vendors menu, choose Pay Bills.
- Check the Deposit that matched the Vendor check amount.
- Select the Set Credit button and apply the Credit you created earlier.
- Then, click Done.
- Proceed to Pay Select Bills and then Done.
I'll be around if you need more help.