negative balance showing once I have recorded payment of customers invoice

Hi Carissa, thanks for joining the Community. 

Do you record the invoice payments manually (by selecting 'Receive payment' against the invoice) or by matching the payment from your connected bank in QuickBooks? 

If you'd prefer, you can contact our Live Support team. They'll have the tools available to set up a screen share with our Smart Look software, where they can view your QuickBooks with you in real time. For more information on how to contact them, please click this link: How to get help with QuickBooks.