It's nice to see you here in the Community, @paul-firstprinci.
Allow me to get you pointed in the right direction to help you in having the Hubstaff payments to reflect in QuckBooks Online.
To guide you with the proper way of syncing the payments from Hubstaff into the system, I recommend contacting their customer service support. They'll be able to walk you through on what are the steps to be taken, so payments will reflect in QBO since they are two different programs.
To add up, you can always utilize this link about recording invoice payments in QuickBooks Online in case you need it in your future transactions: Learn how to receive and categorise invoice payments in QuickBooks Online.
Let me know how the conversations goes or if you have any other concerns. I'll be right here to assist you. Take care!
