Hi Clydegao
Generally speaking, when you look at your bank account you should only have one transaction for a supplier payment (a withdrawal - credit).
If you have a secondary deposit, I would be checking your linked accounts are set up correctly. Ideally, you want to check out Accounting>>Managed linked accounts>>Purchases, in particular, the Liability account for tracking payables. This should be set to an individual account like the Trade Creditors. If that is set to a bank account, you'll find when a payment is made it will be generating a deposit and withdrawal as you are impacting both accounts with the one transaction.
Please note: If you have incorrectly set up the Liability account for tracking payables, you would be looking at deleting all payments and purchases before updating that account and redoing. This ensures that you don'y encounter an reconciliaiton errors in the future with that payable side of things.