QBO connector currently supports Creating a bill, but customers are not able to create payments on that bill as there is no such action.
Pro customer request.
We are planning to add support for custom actions in QuickBooks. This is planned for Mid 2017.
For the benefit of anyone who hasn't seen it yet, we do have this action already. Check it out and let us know if you have any questions about it!
Send us a ticket, we will try our best to assist you with your problem