When we dont have money in the Paypal account, the transaction comes from our bank account through the Paypal account. Quickbooks shows a duplicate.

We have a PayPal account and a bank account. When we dont have money in the Paypal account, the transaction comes from the bank account through the Paypal account. Quickbooks shows a double transaction, which is wrong. It shows money going out of the bank and also money going out of Paypal, when it should be just one transaction. How can we prevent this instead of manually going and excluding all duplicates? Should we always have our PayPal account topped up to stop it from taking money from the bank account?