Thank you for posting here in the Community, @wpwithtom.
In QuickBooks Self-Employed, you can choose to add either the bank connected with PayPal or the app itself. This way, you'll be able to avoid getting the transactions both in negative and positive figures.
Additionally, the transactions that will reflect in the system will depend on the information the bank shares or with PayPal. I suggest logging into your account to verify if both transactions are showing from the list.
If yes, try to review the description to determine if this is a transfer fund from your bank. If verified, QuickBooks automatically detects the status and mark them as a transfer.
That said, it'll not affect the calculation of your purchases. Only the actual transactions with the negative amount need to be categorized into the appropriate expense category.
If you need further assistance, you can also contact the QBSE Support Team. One of them will be able to take over and guide you with the process.
For additional reference, I suggest you visit the following articles related to the information above:
Stay in touch whenever you have additional questions about QBSE. I’m here to make sure you’re taken care of. Have a great rest of the day.
